Publications

PATENTS

  • Çalık P., Ergün B.G., ‘’Modified AOX1 Promoter Variants’’ Publication number: WO/2020/068018, EP2019868082. (Under evaluation)
  • Çalık P., Ergün B.G., ‘’Design of Alcohol Dehydrogenase 2 (ADH2) Promoter Variants by Promotor Engineering’’ Publication number: WO/2020/068019, EP2019864347 (Under evaluation)

SCI PUBLICATIONS

92. Yaman, O.U, Çalık, P., (2023). MachineTFBS: Motif-based method to predict transcription factor binding sites with first-best models from machine learning library, Biochem Eng J. volume: 198 Article 108990. doi: 10.1016/j.bej.2023.108990

91. Yaman, O.U., Avcı, B., Çalık, P., (2022).  Saccharomyces cerevisiae cis-acting DNA sequences curation pipeline (Sc-cADSs-CP): Master transcription factors prediction in yeasts, Biochem Eng J. volume: 188 Article 108673. https://doi.org/10.1016/j.bej.2022.108673

https://authors.elsevier.com/a/1f-1s,V9BZOqNW

90. Ergün B.G., Çalık P., 2021. Hybrid-architectured promoter design to deregulate expression in yeast, Methods in Enzymology. volume: 660 (5), 105-125.

89. Ergün B.G., Çalık P.,  2021. Hybrid architectured promoter design to engineer expression in yeast, Methods in Enzymology. volume: 660 (4), 81-104.

2017-2020

88. Wehbe, O., Yaman, OU, Çalık, P., (2020). Ethanol fed-batch bioreactor operation to enhance therapeutic protein production in Pichia pastoris under hybrid-architectured ADH2 promoter, Biochem Eng J. volume: 164 Article 107782. doi: 10.1016/j.bej.2020.107782

87. Demir, İ., Çalık, P., (2020). Hybrid-architectured double-promoter expression systems enhance and upregulate-deregulated gene expressions in Pichia pastoris in methanol-free media, Applied Microbiology and Biotechnology. 104(19), 8381–8397. doi: 10.1007/s00253-020-10796-5

86. Kalender, Ö., Çalık, P., (2020). Regulatory proteins in central carbon metabolism of Pichia pastoris and Saccharomyces cerevisiae: a comparative analysis, Applied Microbiology and Biotechnology. 104(17), 7273-7311. doi: 1007/s00253-020-10680-2

85. Ergün BG, Demir İ, Özdamar TH, Gasser B, Mattanovich D, Çalık P Engineered deregulation of expression in yeast with designed hybrid-promoter architectures in coordination with discovered master regulator transcription factor (2020) Adv. Biosys. 4(4): 1900172.  DOI:10.1002/adbi.201900172

84. Öztürk, S., Demir, İ.,  Çalık, P.  Isolation of High-Quality RNA from
Pichia pastoris (2019) Current Protocols in Protein Science, 98, e101. doi: 10.1002/cpps.101

83. Gündüz-Ergün, B., Gasser, B., Mattanovich, D., Çalık P. Engineering of alcohol dehydrogenase 2 hybrid-promoter architectures in Pichia pastoris to enhance recombinant protein expression on ethanol (2019) Biotechnol. Bioeng., 116(10), 2674-2686. DOI: 10.1002/bit.27095

82. Gündüz-Ergün, B., Huccetogullari, D., Öztürk, S., Çelik, E., Çalık P. Established and Upcoming Yeast Expression Systems (2019). Methods Mol. Biol. 1923:1–74.

81. Ata, Ö.,  Rebnegger, C., Tatto, N., Valli, M., Mairinger, T., Hann, S., Steiger, M., Çalık, P., Mattanovich, D. A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii  (2018) Nature Communications, Volume 9, Article number: 4911 (2018)

https://www.nature.com/articles/s41467-018-07430-4#disqus_thread

80. Çalık, P., Hoxha, B., Çalık, G., Özdamar, T.H., Hybrid fed-batch bioreactor operation design: Control of substrate uptake enhances recombinant protein production in high-cell-density fermentations (2018)  Journal of Chemical Technology and Biotechnology, 93(11), 3326-2225.

79. Massahi, A., Çalık, P., Naturally occurring novel promoters around pyruvate branch-point for recombinant protein production in Pichia pastoris: Pyruvate decarboxylase- and pyruvate kinase- promoters (2018)  Biochem Eng J. 138, 111-120.

Link: https://authors.elsevier.com/a/1XRq1,V9BZAinu

2017

78. Yaman, S., Çalık, P., Molasses-based feeding strategy enhances recombinant thermostable glucose isomerase production by Escherichia coli BL21 (DE3) ( 2017) Biotechnology and Applied Biochemistry, 64, 944–954.  DOI:10.1002/bab.1549

77. Öztürk, S., Gündüz-Ergün, B.,  Çalık, P.,  Double promoter expression systems for recombinant protein production by industrial microorganisms ( 2017) Applied Microbiology and Biotechnology, 101(20), 7459-7475. DOI: 10.1007/s00253-017-8487-y 

76. Kocabaş¸ P., Çalık, P., Çalık, G., Özdamar,  T.H.,  Analyses of extracellular protein production in Bacillus subtilis: I- Genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data (2017) Biochem Eng J., 127, 229-241. https://doi.org/10.1016/j.bej.2017.07.005

75. Kocabaş¸ P., Çalık, G., Çalık, P., Özdamar, T.H., Analyses of extracellular protein production in Bacillus subtilis: II- Responses of reaction network to oxygen transfer at transcriptional level (2017) Biochem Eng J., 127, 242,261.   https://doi.org/10.1016/j.bej.2017.07.004

74. Ata, Ö., Prielhofer, R., Gasser, B., Mattanovich, D., Çalık, P.,  Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in Pichia pastoris (2017)  Biotechnology & Bioengineering, 114(10), 2319-2327. DOI: 10.1002/bit.26363.

2011-2016

  1. Gündüz-Ergün, B.,  Çalık, P. Lignocellulose degrading extremozymes produced by Pichia pastoris: current status and future prospects (2016) Bioprocess and Biosystems Engineering, 39(1), pp.1-36.
  2. Massahi, A., Çalık, P. Endogenous signal peptides in recombinant protein production by Pichia pastoris: From in-silico analysis to fermentation (2016) Journal of Theoretical Biology, 408, pp. 22-33.
  1. Güneş, H., Çalık, P. Oxygen transfer as a tool for fine-tuning recombinant protein production by Pichia pastoris under glyceraldehyde-3-phosphate dehydrogenase promoter (2016) Bioprocess and Biosystems Engineering, 39 (7), pp. 1061-1072.
  1. Öztürk, S., Çalık, P., Özdamar, T.H. Fed-Batch Biomolecule Production by Bacillus subtilis: A State of the Art Review (2016) Trends in Biotechnology, 34 (4), pp. 329-345.
  1. Güneş, H., Boy, E., Ata, O., Zerze, G.H., Çalık, P., Özdamar, T.H. Methanol feeding strategy design enhances recombinant human growth hormone production by Pichia pastoris (2016) Journal of Chemical Technology and Biotechnology, 91 (3), pp. 664-671.
  1. Çalık, G., Kocabaş, P., Afşar, H., Çalık, P., Özdamar, T.H. Parametric continuous feed stream design to fine-tune fed-batch bioreactor performance: Recombinant human growth hormone production in Bacillus subtilis (2016) Journal of Chemical Technology and Biotechnology, 91, pp.2740-2750.
  1. Şahin, B., Öztürk, S., Çalık, P., Özdamar, T.H. Feeding strategy design for recombinant human growth hormone production by Bacillus subtilis (2015) Bioprocess and Biosystems Engineering, 38 (10), pp. 1855-1865.
  1. Ata, Ö., Boy, E., Güneş, H., Çalık, P. Codon optimization of xylA gene for recombinant glucose isomerase production in Pichia pastoris and fed-batch feeding strategies to fine-tune bioreactor performance (2015) Bioprocess and Biosystems Engineering, 38 (5), art. no. 1333, pp. 889-903.
  1. Çalık, P., Ata, T., Güneş, H., Massahi, A., Boy, E., Keskin, A., Öztürk, S., Zerze, G.H., Özdamar, T.H. Recombinant protein production in Pichia pastoris under glyceraldehyde-3-phosphate dehydrogenase promoter: From carbon source metabolism to bioreactor operation parameters (2015) Biochemical Engineering Journal, 95, pp. 20-36.
  1. Massahi, A., Çalık, P. In-silico determination of Pichia pastoris signal peptides for extracellular recombinant protein production (2015) Journal of Theoretical Biology, 364, pp. 179-188.
  1. Akdağ, B., Çalık, P. Recombinant protein production by sucrose-utilizing escherichia coli W: Untreated beet molasses-based feeding strategy development (2015) Journal of Chemical Technology and Biotechnology, 90 (6), pp. 1070-1076.
  1. Eskitoros, M.S., Çalık, P. Co-substrate mannitol feeding strategy design in semi-batch production of recombinant human erythropoietin production by Pichia pastoris (2014) Journal of Chemical Technology and Biotechnology, 89 (5), pp. 644-651.
  1. Eskitoros, M.S., Ata, O., Çalık, P. Metabolic reaction network of Pichia pastoris with glycosylation reactions: Flux analysis for erythropoietin production (2014) Journal of Chemical Technology and Biotechnology, 89 (11), pp. 1675-1685.
  1. Çalık, P., Bozkurt, B., Zerze, G.H., Inankur, B., Bayraktar, E., Boy, E., Orman, M.A., Açik, E., Özdamar, T.H. Effect of co-substrate sorbitol different feeding strategies on human growth hormone production by recombinant Pichia pastoris (2013) Journal of Chemical Technology and Biotechnology, 88 (9), pp. 1631-1640.
  1. Angardi, V., Çalık, P. Beet molasses based exponential feeding strategy for thermostable glucose isomerase production by recombinant Escherichia coli BL21 (DE3) (2013) Journal of Chemical Technology and Biotechnology, 88 (5), pp. 845-852.
  1. Çelik, E., Çalık, P. Production of recombinant proteins by yeast cells (2012) Biotechnology Advances, 30 (5), pp. 1108-1118.  Invited Review 
  1. Guven, B., Boyaci, I.H., Tamer, U., Çalık, P. A rapid method for detection of genetically modified organisms based on magnetic separation and surface-enhanced Raman scattering (2012) Analyst, 137 (1), pp. 202-208.
  1. Soyaslan, E.T., Çalık, P. Enhanced recombinant human erythropoietin production by Pichia pastoris in methanol fed-batch/sorbitol batch fermentation through pH optimization (2011) Biochemical Engineering Journal, 55 (1), pp. 59-65.
  1. Çalık, P., Şahin, M., Taşpinar, H., Soyaslan, E.Ş., Inankur, B. Dynamic flux balance analysis for pharmaceutical protein production by Pichia pastoris: Human growth hormone (2011) Enzyme and Microbial Technology, 48 (3), pp. 209-216.

1998-2010

  1. Çalık, P., Bayraktar, E., Inankur, B., Soyaslan, E.Ş., Şahin, M., Taşpinar, H., Açik, E., Yilmaz, R., Özdamar, T.H. Influence of pH on recombinant human growth hormone production by Pichia pastoris (2010) Journal of Chemical Technology and Biotechnology, 85 (12), pp. 1628-1635.
  1. Çelik, E., Çalık, P., Oliver, S.G. Metabolic flux analysis for recombinant protein production by Pichia pastoris using dual carbon sources: Effects of methanol feeding rate (2010) Biotechnology and Bioengineering, 105 (2), pp. 317-329.
  1. Çalık, P., Inankur, B., Soyaslan, E.Ş., Şahin, M., Taşpinar, H., Açik, E., Bayraktar, E. Fermentation and oxygen transfer characteristics in recombinant human growth hormone production by Pichia pastoris in sorbitol batch and methanol fed-batch operation (2010) Journal of Chemical Technology and Biotechnology, 85 (2), pp. 226-233.
  1. Çalık, P., Balci, O., Özdamar, T.H. Human growth hormone-specific aptamer identification using improved oligonucleotide ligand evolution method (2010) Protein Expression and Purification, 69 (1), pp. 21-28.
  1. Özdamar, T.H., Şentürk, B., Yilmaz, O.D., Kocabaş, P., Çalık, G., Çalık, P. Bioreaction network flux analysis for human protein producing Bacillus subtilis based on genome-scale model (2010) Chemical Engineering Science, 65 (1), pp. 574-580.
  1. Çelik, E., Çalık, P., Oliver, S.G. Fed-batch methanol feeding strategy for recombinant protein production by Pichia pastoris in the presence of co-substrate sorbitol (2009) Yeast, 26 (9), pp. 473-484.
  1. Çalık, P., Levent, H. Effects of pulse feeding of beet molasses on recombinant benzaldehyde lyase production by Escherichia coli BL21(DE3) (2009) Applied Microbiology and Biotechnology, 85 (1), pp. 65-73.
  1. Çalık, P., Levent, H. Effects of pretreated beet molasses on benzaldehyde lyase production by recombinant Escherichia coli BL21(DE3)pLySs (2009) Journal of Applied Microbiology, 107 (5), pp. 1536-1541.
  1. Kocabaş, P., Çalık, P., Çalık, G., Özdamar, T.H. Microarray studies in Bacillus subtilis (2009) Biotechnology Journal, 4 (7), pp. 1012-1027.
  1. Kaya-Çeliker, H., Angardi, V., Çalık, P. Regulatory effects of oxygen transfer on overexpression of recombinant benzaldehyde lyase production by Escherichia coli BL21 (DE3) (2009) Biotechnology Journal, 4 (7), pp. 1066-1076.
  1. Çelik, E., Çalık, P., Oliver, S.G. A structured kinetic model for recombinant protein production by Mut+ strain of Pichia pastoris (2009) Chemical Engineering Science, 64 (23), pp. 5028-5035.
  1. Geçkil, H., Çalık, P. Editorial: Biotech in Turkey. (2009) Biotechnology journal, 4 (7), p. 951.
  1. Orman, M.A., Çalık, P., Özdamar, T.H. The influence of carbon sources on recombinant-human-growth-hormone production by Pichia pastoris is dependent on phenotype: A comparison of Muts and Mut+ strains (2009) Biotechnology and Applied Biochemistry, 52 (3), pp. 245-255.
  1. Çalık, P., Angardi, V., Haykir, N.I., Boyaci, I.H. Glucose isomerase production on a xylan-based medium by Bacillus thermoantarcticus (2009) Biochemical Engineering Journal, 43 (1), pp. 8-15.
  1. Özdamar, T.H., Şentürk, B., Yilmaz, Ö.D., Çalık, G., Çelik, E., Çalık, P. Expression system for recombinant human growth hormone production from Bacillus subtilis (2009) Biotechnology Progress, 25 (1), pp. 75-84.
  1. Ölçeroğlu, A.H., Çalık, P., Yilmaz, L. Development of enhanced ultrafiltration methodologies for the resolution of racemic benzoin (2008) Journal of Membrane Science, 322 (2), pp. 446-452.
  1. Eda Çelik, S., Ozbay, N., Oktar, N., Çalık, P. Use of biodiesel byproduct crude glycerol as the carbon source for fermentation processes by recombinant Pichia pastoris (2008) Industrial and Engineering Chemistry Research, 47 (9), pp. 2985-2990.
  1. Çalık, P., Orman, M.A., Çelik, E., Halloran, S.M., Çalık, G., Özdamar, T.H. Expression system for synthesis and purification of recombinant human growth hormone in Pichia pastoris and structural analysis by MALDI-ToF mass spectrometry (2008) Biotechnology Progress, 24 (1), pp. 221-226.
  1. Çelik, E., Çalık, P., Halloran, S.M., Oliver, S.G. Production of recombinant human erythropoietin from Pichia pastoris and its structural analysis (2007) Journal of Applied Microbiology, 103 (6), pp. 2084-2094.
  1. Çalık, P., Ileri, N. pH influences intracellular reaction network of β-lactamase producing Bacillus licheniformis (2007) Chemical Engineering Science, 62 (18-20), pp. 5206-5211.
  1. Ileri, N., Çalık, P., Şengül, A. Phosphate enrichment and fed-batch operation for prolonged β-lactamase production by Bacillus licheniformis (2007) Journal of Applied Microbiology, 102 (5), pp. 1418-1426.
  1. Olceroglu, A.H., Çalık, P., Yilmaz, L. Chiral separation of racemic benzoin via enzyme enhanced ultrafiltration (2006) Desalination, 200 (1-3), pp. 464-465.

 

  1. Namaldi, A., Çalık, P., Uludag, Y. Effects of spray drying temperature and additives on the stability of serine alkaline protease powders (2006) Drying Technology, 24 (11), pp. 1495-1500.
  1. Kocabaş, P., Çalık, P., Özdamar, T.H. Fermentation characteristics of l-tryptophan production by thermoacidophilic Bacillus acidocaldarius in a defined medium (2006) Enzyme and Microbial Technology, 39 (5), pp. 1077-1088.
  1. Çalık, P., Yilgör, P., Demir, A.S. Influence of controlled-pH and uncontrolled-pH operations on recombinant benzaldehyde lyase production by Escherichia coli (2006) Enzyme and Microbial Technology, 38 (5), pp. 617-627
  1. Ileri, N., Çalık, P. Effects of pH strategy on endo- and exo-metabolome profiles and sodium potassium hydrogen ports of β-lactamase-producing Bacillus licheniformis (2006) Biotechnology Progress, 22 (2), pp. 411-419.
  1. Çalık, P., Ileri, N., Erdinç, B.I., Aydogan, N., Argun, M. Novel antifoam for fermentation processes: Fluorocarbon-hydrocarbon hybrid unsymmetrical bolaform surfactant (2005) Langmuir, 21 (19), pp. 8613-8619.
  1. Çalık, P., Arifoǧlu, M., Çalık, G. Oxygen transfer effects in β-lactamase fermentation by Bacillus licheniformis in a glucose-based defined medium (2005) Journal of Chemical Technology and Biotechnology, 80 (9), pp. 1062-1071.
  1. Özçelik, I.Ş., Çalık, P., Çalık, G., Özdamar, T.H. Metabolic engineering of aromatic group amino acid pathway in Bacillus subtilis for L-phenylalanine production (2004) Chemical Engineering Science, 59 (22-23), pp. 5019-5026.
  1. Çalık, G., Pehlivan, N., Özçelik, I.Ş., Çalık, P., Özdamar, T.H. Fermentation and oxygen transfer characteristics in serine alkaline protease production by recombinant Bacillus subtilis in molasses-based complex medium (2004) Journal of Chemical Technology and Biotechnology, 79 (11), pp. 1243-1250.
  1. Çalık, P., Yilgör, P., Ayhan, P., Demir, A.S. Oxygen transfer effects on recombinant benzaldehyde lyase production (2004) Chemical Engineering Science, 59 (22-23), pp. 5075-5083.
  1. Çelik, E., Çalık, P. Bioprocess parameters and oxygen transfer characteristics in β-lactamase production by Bacillus species (2004) Biotechnology Progress, 20 (2), pp. 491-499.
  1. Çalık, P., Bilir, E., Özçelik, I.Ş., Çalık, G., Özdamar, T.H. Inorganic compounds have dual effect on recombinant protein production: Influence of anions and cations on serine alkaline protease production (2004) Journal of Applied Microbiology, 96 (1), pp. 194-200.
  1. Çalık, P., Kalender, N., Özdamar, T.H. Overexpression of serine alkaline protease encoding gene in Bacillus species: Performance analyses (2003) Enzyme and Microbial Technology, 33 (7), pp. 967-974.
  1. Çalık, P., Çelik, E., Telli, I.E., Oktar, C., Özdemir, E. Protein-based complex medium design for recombinant serine alkaline protease production (2003) Enzyme and Microbial Technology, 33 (7), pp. 975-986.
  1. Çalık, P., Tomlin, G.C., Oliver, S.G., Özdamar, T.H. Overexpression of a serine alkaline protease gene in Bacillus licheniformis and its impact on the metabolic reaction network (2003) Enzyme and Microbial Technology, 32 (6), pp. 706-720.
  1. Çalık, G., Pehlivan, N., Kalender, N., Özdamar, T.H., Çalık, P. Utilization of pretreated molasses for serine alkaline protease production with recombinant Bacillus species (2003) Chemical Engineering Communications, 190 (5-8), pp. 630-644.
  1. Çalık, P., Bayram, A., Özdamar, T.H. Regulatory effects of alanine-group amino acids on serine alkaline protease production by recombinant Bacillus licheniformis (2003) Biotechnology and Applied Biochemistry, 37 (2), pp. 165-171.
  1. Çalık, P., Bilir, E., Çalık, G., Özdamar, T.H. Bioreactor operation parameters as tools for metabolic regulations in fermentation processes: Influence of pH conditions (2003) Chemical Engineering Science, 58 (3-6), pp. 759-766.
  1. Çalık, P., Şenver Özçelik, I., Çalık, G., Özdamar, T.H. Enzyme-ion exchanger interactions in serine alkaline protease separation: Theory, equilibria and kinetics (2002) Biochemical Engineering Journal, 12 (3), pp. 193-204.
  1. Çalık, P., Bilir, E., Çalık, G., Özdamar, T.H. Influence of pH conditions on metabolic regulations in serine alkaline protease production by Bacillus licheniformis (2002) Enzyme and Microbial Technology, 31 (5), pp. 685-697.
  1. Çalık, P., Özdamar, T.H. Bioreaction network flux analysis for industrial microorganisms: A review (2002) Reviews in Chemical Engineering, 18 (6), pp. 553-596.
  1. Çalık, P., Özdamar, T.H. Metabolic flux analysis for human therapeutic protein productions and hypothesis for new therapeutical strategies in medicine (2002) Biochemical Engineering Journal, 11 (1), pp. 49-68.
  1. Çalık, P., Çalık, G., Özdamar, T.H. Bioprocess development for serine alkaline protease production: A review (2001) Reviews in Chemical Engineering, 17 (4 SUPPL.), pp. 1-59.
  1. Çalık, P., Özdamar, T.H. Carbon sources affect metabolic capacities of Bacillus species for the production of industrial enzymes: Theoretical analyses for serine and neutral proteases and α-amylase (2001) Biochemical Engineering Journal, 8 (1), pp. 61-81.
  1. Çalık, P., Çalık, G., Takaç, S., Özdamar, T.H. Metabolic flux analyses for serine alkaline protease production (2000) Enzyme and Microbial Technology, 27 (10), pp. 793-805.
  1. Çalık, P., Çalık, G., Özdamar, T.H. Oxygen-transfer strategy and its regulation effects in serine alkaline protease production by Bacillus licheniformis (2000) Biotechnology and Bioengineering, 69 (3), pp. 301-311.
  1. Çalık, P., Akbay, A. Mass flux balance-based model and metabolic flux analysis for collagen synthesis in the fibrogenesis process of human liver (2000) Medical Hypotheses, 55 (1), pp. 5-14.
  1. Takaç, S., Elmas, S., Çalık, P., Özdamar, T.H. Separation of the protease enzymes of Bacillus licheniformis from the fermentation medium by crossflow ultrafiltration (2000) Journal of Chemical Technology and Biotechnology, 75 (6), pp. 491-499.
  1. Çalık, P., Takaç, S., Çalık, G., Özdamar, T.H. Serine alkaline protease overproduction capacity of Bacillus licheniformis (2000) Enzyme and Microbial Technology, 26 (1), pp. 45-60.
  1. Çalık, P., Çalık, G., Takaç, S., Özdamar, T.H. Metabolic flux analysis for serine alkaline protease fermentation by Bacillus licheniformis in a defined medium: Effects of the oxygen transfer rate (1999) Biotechnology and Bioengineering, 64 (2), pp. 151-167.
  1. Çalık, P., Özdamar, T.H. Mass flux balance-based model and metabolic pathway engineering analysis for serine alkaline protease synthesis by Bacillus licheniformis (1999) Enzyme and Microbial Technology, 24 (10), pp. 621-635.
  1. Çalık, G., Savaşçi, H., Çalık, P., Özdamar, T.H. Growth and κ-carrageenan immobilization of Pseudomonas dacunhae cells for L-alanine production (1999) Enzyme and Microbial Technology, 24 (1-2), pp. 67-74.
  1. Çalık, P., Çalík, G., Özdamar, T.H. Oxygen transfer effects in serine alkaline protease fermentation by Bacillus licheniformis: Use of citric acid as the carbon source (1998) Enzyme and Microbial Technology, 23 (7-8), pp. 451-461.
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