{"id":8,"date":"2016-09-13T16:54:24","date_gmt":"2016-09-13T16:54:24","guid":{"rendered":"http:\/\/blog.metu.edu.tr\/indbio\/?page_id=8"},"modified":"2026-02-22T14:01:28","modified_gmt":"2026-02-22T14:01:28","slug":"publications","status":"publish","type":"page","link":"https:\/\/blog.metu.edu.tr\/indbio\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<p><strong>PATENTS<\/strong><\/p>\n<ul>\n<li><strong>\u00c7al\u0131k P<\/strong>., Erg\u00fcn B.G., 1.07.2025. \u2018\u2019Modified AOX1 Promoter Variants\u2019\u2019 Publication number: WO\/2020\/068018, US12344848B2.<br \/>\n.<\/li>\n<li><strong>\u00c7al\u0131k P<\/strong>., Erg\u00fcn B.G., 17.09.2024. \u2018\u2019Design of Alcohol Dehydrogenase 2 (ADH2) Promoter Variants by Promotor Engineering\u2019\u2019, US12091658B2.<\/li>\n<\/ul>\n<p><strong>SCI PUBLICATIONS<\/strong><\/p>\n<p>95. Wei Xigang, Cong Wenjie, Zhou Hualan, Zhang Jianguo, <strong>\u00c7al\u0131k P.<\/strong>, 2026. Decode and Rewire: Programming <em>Komagataella phaffii<\/em> for Bioproduction with Synthetic Transcriptional Tools. <strong>Trends in Biotechnology<\/strong><em>.\u00a0<\/em><a class=\"anchor doi anchor-primary\" title=\"Persistent link using digital object identifier\" href=\"https:\/\/doi.org\/10.1016\/j.tibtech.2025.12.009\" target=\"_blank\" rel=\"noreferrer noopener\" aria-label=\"Persistent link using digital object identifier\"><span class=\"anchor-text-container\"><span class=\"anchor-text\">https:\/\/doi.org\/10.1016\/j.tibtech.2025.12.009<\/span><\/span><\/a><\/p>\n<div class=\"LicenseInfo text-xs u-margin-xs-bottom access-type-label-only\">\n<div class=\"AccessLabel\"><span style=\"font-size: revert;color: initial\">94. Avc\u0131, B<\/span><strong style=\"font-size: revert;color: initial\">, <\/strong><strong style=\"font-size: revert;color: initial\">\u00c7al\u0131k, P<\/strong><span style=\"font-size: revert;color: initial\">.,2025. Dual-acting single-engineered hybrid-architectured promoters <\/span><strong style=\"font-size: revert;color: initial\">enhance and convert expressions into multi-carbon source-regulated systems in <\/strong><em style=\"font-size: revert;color: initial\">Komagataella phaffii, <\/em><em style=\"font-size: revert;color: initial\">Enzyme and Microbial Technology<\/em><span style=\"font-size: revert;color: initial\">. volume: 191 Article 110713. https:\/\/doi.org\/10.1016\/j.enzmictec.2025.110713<\/span><\/div>\n<\/div>\n<p>93. Raja, W.A, <strong>\u00c7al\u0131k, P.,<\/strong> (2025). Biochemical production from sustainable carbon 2ources by <em>Komagataella phaffii<\/em>, Biochem Eng J. volume: 219 Article 109702. https:\/\/doi.org\/10.1016\/j.bej.2025.109702<\/p>\n<p>92. Yaman, O.U, <strong>\u00c7al\u0131k, P.,<\/strong> (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.\u00a0<a href=\"https:\/\/doi.org\/10.1016\/j.bej.2023.108990\">doi: 10.1016\/j.bej.2023.108990<\/a><\/p>\n<p>91. Yaman, O.U., Avc\u0131, B., <strong>\u00c7al\u0131k, P.,<\/strong> (2022).\u00a0 <span class=\"title-text\"><em>Saccharomyces cerevisiae cis-<\/em>acting DNA sequences curation pipeline (<em>Sc-c<\/em>ADSs-CP): Master transcription factors prediction in yeasts, <\/span>Biochem Eng J. volume: 188 Article 108673. https:\/\/doi.org\/10.1016\/j.bej.2022.108673<\/p>\n<h4><strong>https:\/\/authors.elsevier.com\/a\/1f-1s,V9BZOqNW<\/strong><\/h4>\n<p>90. Erg\u00fcn B.G., <strong>\u00c7al\u0131k P.,<\/strong> 2021. Hybrid-architectured promoter design to deregulate expression in yeast, Methods in Enzymology. volume: 660 (5), 105-125.<\/p>\n<p>89. Erg\u00fcn B.G., <strong>\u00c7al\u0131k P.,<\/strong> \u00a02021. Hybrid architectured promoter design to engineer expression in yeast, Methods in Enzymology. volume: 660 (4), 81-104.<\/p>\n<p><strong>2017-2020<\/strong><\/p>\n<p>88. Wehbe, O., Yaman, OU, <strong>\u00c7al\u0131k, P.,<\/strong> (2020).\u00a0Ethanol fed-batch bioreactor operation to enhance therapeutic protein production in <em>Pichia pastoris<\/em> under hybrid-architectured <em>ADH2<\/em> promoter<strong>,<\/strong> Biochem Eng J. volume: 164 Article 107782. doi: <a id=\"doiLink\" class=\"els-external-link\" href=\"https:\/\/doi.org\/10.1016\/j.bej.2020.107782\" target=\"_blank\" rel=\"noopener noreferrer\">10.1016\/j.bej.2020.107782<\/a><\/p>\n<p>87. Demir, \u0130., <strong>\u00c7al\u0131k, P.,<\/strong> (2020). Hybrid-architectured double-promoter expression systems enhance and upregulate-deregulated gene expressions in <em>Pichia pastoris<\/em>\u00a0in methanol-free media<strong>,<\/strong> Applied Microbiology and Biotechnology. 104(19), 8381\u20138397. doi: <a href=\"https:\/\/sqrl.metu.edu.tr\/src\/read_body.php?mailbox=INBOX&amp;passed_id=145324&amp;startMessage=1\">10.1007\/s00253-020-10796-5<\/a><\/p>\n<p>86. Kalender, \u00d6., <strong>\u00c7al\u0131k, P.,<\/strong> (2020). Regulatory proteins in central carbon metabolism of <em>Pichia<\/em> <em>pastoris<\/em> and <em>Saccharomyces cerevisiae<\/em>: a comparative analysis<strong>,<\/strong> Applied Microbiology and Biotechnology. 104(17), 7273-7311. doi: 1007\/s00253-020-10680-2<\/p>\n<p>85. Erg\u00fcn BG, Demir \u0130, \u00d6zdamar TH, Gasser B, Mattanovich D, <strong>\u00c7al\u0131k P<\/strong> 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. \u00a0DOI:10.1002\/adbi.201900172<\/p>\n<p>84. \u00d6zt\u00fcrk, S., Demir, \u0130.,\u00a0 <strong>\u00c7al\u0131k, P.<\/strong>\u00a0 Isolation of High-Quality RNA from<br \/>\n<em>Pichia pastoris<\/em> (2019) Current Protocols in Protein Science, 98, e101. doi: 10.1002\/cpps.101<\/p>\n<p>83. G\u00fcnd\u00fcz-Erg\u00fcn, B., Gasser, B., Mattanovich, D., <strong>\u00c7al\u0131k P.<\/strong> Engineering of alcohol dehydrogenase 2 hybrid-promoter architectures in <em>Pichia pastoris<\/em> to enhance recombinant protein expression on ethanol (2019)\u00a0<em>B<\/em>iotechnol. Bioeng.<em>, 116(10), 2674-2686. DOI: 10.1002\/bit.27095<\/em><\/p>\n<p>82. G\u00fcnd\u00fcz-Erg\u00fcn, B., Huccetogullari, D., \u00d6zt\u00fcrk, S., \u00c7elik, E., <strong>\u00c7al\u0131k P.<\/strong> Established and Upcoming Yeast Expression Systems (2019). Methods Mol. Biol. <strong>1923<\/strong>:1\u201374.<\/p>\n<p>81. Ata,\u00a0\u00d6.,\u00a0 Rebnegger, C., Tatto, N., Valli, M., Mairinger, T., Hann, S., Steiger, M., <strong>\u00c7al\u0131k, P.<\/strong>, Mattanovich, D. A single Gal4-like transcription factor activates the Crabtree effect in\u00a0<em>Komagataella phaffii\u00a0\u00a0(2018)<\/em>\u00a0Nature Communications, Volume\u00a09, Article\u00a0number:\u00a04911\u00a0(2018)<\/p>\n<p>https:\/\/www.nature.com\/articles\/s41467-018-07430-4#disqus_thread<\/p>\n<p>80.<strong> \u00c7al\u0131k, P.<\/strong>, Hoxha, B., \u00c7al\u0131k, G., \u00d6zdamar, T.H., Hybrid fed-batch bioreactor operation design: Control of substrate uptake enhances recombinant protein production in high-cell-density fermentations (<em>2018<\/em>)\u00a0 Journal of Chemical Technology and Biotechnology,\u00a093(11), 3326-2225.<\/p>\n<p>79. Massahi, A., <strong>\u00c7al\u0131k, P<\/strong>., Naturally occurring novel promoters around pyruvate branch-point for recombinant protein production in <em>Pichia pastoris<\/em>: Pyruvate decarboxylase- and pyruvate kinase- promoters\u00a0(<em>2018<\/em>)\u00a0\u00a0Biochem Eng J. 138, 111-120.<\/p>\n<p>Link:\u00a0https:\/\/authors.elsevier.com\/a\/1XRq1,V9BZAinu<\/p>\n<p><strong>2017<\/strong><\/p>\n<p>78. Yaman, S.,\u00a0<strong>\u00c7al\u0131k, P.,<\/strong> Molasses-based feeding strategy enhances recombinant thermostable glucose isomerase production by\u00a0<em>Escherichia coli<\/em>\u00a0BL21 (DE3) (<em>\u00a02017<\/em>) Biotechnology and Applied Biochemistry, 64, 944\u2013954.\u00a0 DOI:10.1002\/bab.1549<\/p>\n<p>77. \u00d6zt\u00fcrk, S., G\u00fcnd\u00fcz-Erg\u00fcn, B.,\u00a0 <strong>\u00c7al\u0131k, P.,<\/strong> \u00a0Double promoter expression systems for recombinant protein production by industrial microorganisms (<em>\u00a02017<\/em>) Applied Microbiology and Biotechnology,<em>\u00a0<\/em>101(20), 7459-7475.<em>\u00a0<strong>DOI: <\/strong>10.1007\/s00253-017-8487-y\u00a0<\/em><\/p>\n<p>76. Kocaba\u015f\u00b8 P., <strong>\u00c7al\u0131k, P<\/strong>., \u00c7al\u0131k, G., \u00d6zdamar,\u00a0 T.H., \u00a0Analyses of extracellular protein production in <em>Bacillus subtilis<\/em>: I- Genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data (2017) Biochem Eng J., 127, 229-241.\u00a0<a href=\"https:\/\/doi.org\/10.1016\/j.bej.2017.07.005\">https:\/\/doi.org\/10.1016\/j.bej.2017.07.005<\/a><\/p>\n<p>75. Kocaba\u015f\u00b8 P., \u00c7al\u0131k, G., <strong>\u00c7al\u0131k, P<\/strong>., \u00d6zdamar, T.H., Analyses of extracellular protein production in <em>Bacillus subtilis<\/em>: II- Responses of reaction network to oxygen transfer at transcriptional level (2017)<strong>\u00a0<\/strong>Biochem Eng J., 127, 242,261.\u00a0\u00a0\u00a0https:\/\/doi.org\/10.1016\/j.bej.2017.07.004<\/p>\n<p>74. Ata, \u00d6., Prielhofer, R., Gasser, B., Mattanovich, D.,\u00a0<strong>\u00c7al\u0131k, P<\/strong>., \u00a0Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in\u00a0<em>Pichia pastoris<\/em>\u00a0(2017) \u00a0Biotechnology &amp; Bioengineering, 114(10), 2319-2327. DOI: 10.1002\/bit.26363.<\/p>\n<p><strong>2011-2016<\/strong><\/p>\n<ol start=\"73\">\n<li>G\u00fcnd\u00fcz-Erg\u00fcn, B.,\u00a0 <strong>\u00c7al\u0131k, P.<\/strong>\u00a0Lignocellulose degrading extremozymes produced by\u00a0Pichia pastoris: current status and future prospects\u00a0(2016) Bioprocess and Biosystems Engineering, 39(1), pp.1-36.<\/li>\n<li>Massahi, A., <strong>\u00c7al\u0131k, P. <\/strong>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.<\/li>\n<\/ol>\n<ol start=\"71\">\n<li>G\u00fcne\u015f, H., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"70\">\n<li>\u00d6zt\u00fcrk, S., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, T.H. Fed-Batch Biomolecule Production by Bacillus subtilis: A State of the Art Review (2016) Trends in Biotechnology, 34 (4), pp. 329-345.<\/li>\n<\/ol>\n<ol start=\"69\">\n<li>G\u00fcne\u015f, H., Boy, E., Ata, O., Zerze, G.H., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"68\">\n<li>\u00c7al\u0131k, G., Kocaba\u015f, P., Af\u015far, H., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"67\">\n<li>\u015eahin, B., \u00d6zt\u00fcrk, S., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, T.H. Feeding strategy design for recombinant human growth hormone production by Bacillus subtilis (2015) Bioprocess and Biosystems Engineering, 38 (10), pp. 1855-1865.<\/li>\n<\/ol>\n<ol start=\"66\">\n<li>Ata, \u00d6., Boy, E., G\u00fcne\u015f, H., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"65\">\n<li><strong>\u00c7al\u0131k, P.<\/strong>, Ata, T., G\u00fcne\u015f, H., Massahi, A., Boy, E., Keskin, A., \u00d6zt\u00fcrk, S., Zerze, G.H., \u00d6zdamar, T.H.\u00a0Recombinant 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.<\/li>\n<\/ol>\n<ol start=\"64\">\n<li>Massahi, A., <strong>\u00c7al\u0131k, P. <\/strong>In-silico determination of Pichia pastoris signal peptides for extracellular recombinant protein production (2015) Journal of Theoretical Biology, 364, pp. 179-188.<\/li>\n<\/ol>\n<ol start=\"63\">\n<li>Akda\u011f, B., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"62\">\n<li>Eskitoros, M.S., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"61\">\n<li>Eskitoros, M.S., Ata, O., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"60\">\n<li><strong>\u00c7al\u0131k, P.<\/strong>, Bozkurt, B., Zerze, G.H., Inankur, B., Bayraktar, E., Boy, E., Orman, M.A., A\u00e7ik, E., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"59\">\n<li>Angardi, V., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"58\">\n<li>\u00c7elik, E., <strong>\u00c7al\u0131k, P.<\/strong> Production of recombinant proteins by yeast cells (2012) Biotechnology Advances, 30 (5), pp. 1108-1118. \u00a0<em><strong>Invited Review\u00a0<\/strong><\/em><\/li>\n<\/ol>\n<ol start=\"57\">\n<li>Guven, B., Boyaci, I.H., Tamer, U., <strong>\u00c7al\u0131k, P. <\/strong>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.<\/li>\n<\/ol>\n<ol start=\"56\">\n<li>Soyaslan, E.T., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"55\">\n<li><strong>\u00c7al\u0131k, P.<\/strong>, \u015eahin, M., Ta\u015fpinar, H., Soyaslan, E.\u015e., 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.<\/li>\n<\/ol>\n<p><strong>1998-2010<\/strong><\/p>\n<ol start=\"54\">\n<li><strong>\u00c7al\u0131k, P.<\/strong>, Bayraktar, E., Inankur, B., Soyaslan, E.\u015e., \u015eahin, M., Ta\u015fpinar, H., A\u00e7ik, E., Yilmaz, R., \u00d6zdamar, T.H. Influence of pH on recombinant human growth hormone production by Pichia pastoris\u00a0(2010) Journal of Chemical Technology and Biotechnology, 85 (12), pp. 1628-1635.<\/li>\n<\/ol>\n<ol start=\"53\">\n<li>\u00c7elik, E., <strong>\u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"52\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Inankur, B., Soyaslan, E.\u015e., \u015eahin, M., Ta\u015fpinar, H., A\u00e7ik, 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.<\/li>\n<\/ol>\n<ol start=\"51\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Balci, O., \u00d6zdamar, T.H. Human growth hormone-specific aptamer identification using improved oligonucleotide ligand evolution method (2010) Protein Expression and Purification, 69 (1), pp. 21-28.<\/li>\n<\/ol>\n<ol start=\"50\">\n<li>\u00d6zdamar, T.H., \u015eent\u00fcrk, B., Yilmaz, O.D., Kocaba\u015f, P., \u00c7al\u0131k, G., <strong>\u00c7al\u0131k, P.<\/strong> Bioreaction network flux analysis for human protein producing Bacillus subtilis based on genome-scale model (2010) Chemical Engineering Science, 65 (1), pp. 574-580.<\/li>\n<\/ol>\n<ol start=\"49\">\n<li>\u00c7elik, E., <strong>\u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"48\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"47\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"46\">\n<li>Kocaba\u015f, P., <strong>\u00c7al\u0131k, P.<\/strong>, \u00c7al\u0131k, G., \u00d6zdamar, T.H. Microarray studies in Bacillus subtilis\u00a0(2009) Biotechnology Journal, 4 (7), pp. 1012-1027.<\/li>\n<\/ol>\n<ol start=\"45\">\n<li>Kaya-\u00c7eliker, H., Angardi, V., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"44\">\n<li>\u00c7elik, E., <strong>\u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"43\">\n<li>Ge\u00e7kil, H., <strong>\u00c7al\u0131k, P.<\/strong> Editorial: Biotech in Turkey. (2009) Biotechnology journal, 4 (7), p. 951.<\/li>\n<\/ol>\n<ol start=\"42\">\n<li>Orman, M.A., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"41\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"40\">\n<li>\u00d6zdamar, T.H., \u015eent\u00fcrk, B., Yilmaz, \u00d6.D., \u00c7al\u0131k, G., \u00c7elik, E., <strong>\u00c7al\u0131k, P. <\/strong>Expression system for recombinant human growth hormone production from Bacillus subtilis (2009) Biotechnology Progress, 25 (1), pp. 75-84.<\/li>\n<\/ol>\n<ol start=\"39\">\n<li>\u00d6l\u00e7ero\u011flu, A.H., <strong>\u00c7al\u0131k, P.<\/strong>, Yilmaz, L. Development of enhanced ultrafiltration methodologies for the resolution of racemic benzoin (2008) Journal of Membrane Science, 322 (2), pp. 446-452.<\/li>\n<\/ol>\n<ol start=\"38\">\n<li>Eda \u00c7elik, S., Ozbay, N., Oktar, N., <strong>\u00c7al\u0131k, P.<\/strong> 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.<\/li>\n<\/ol>\n<ol start=\"37\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Orman, M.A., \u00c7elik, E., Halloran, S.M., \u00c7al\u0131k, G., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"36\">\n<li>\u00c7elik, E., <strong>\u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"35\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Ileri, N. pH influences intracellular reaction network of \u03b2-lactamase producing Bacillus licheniformis (2007) Chemical Engineering Science, 62 (18-20), pp. 5206-5211.<\/li>\n<\/ol>\n<ol start=\"34\">\n<li>Ileri, N., <strong>\u00c7al\u0131k, P.<\/strong>, \u015eeng\u00fcl, A. Phosphate enrichment and fed-batch operation for prolonged \u03b2-lactamase production by Bacillus licheniformis (2007) Journal of Applied Microbiology, 102 (5), pp. 1418-1426.<\/li>\n<\/ol>\n<ol start=\"33\">\n<li>Olceroglu, A.H., <strong>\u00c7al\u0131k, P.<\/strong>, Yilmaz, L. Chiral separation of racemic benzoin via enzyme enhanced ultrafiltration (2006) Desalination, 200 (1-3), pp. 464-465.<\/li>\n<\/ol>\n<p><strong>\u00a0<\/strong><\/p>\n<ol start=\"32\">\n<li>Namaldi, A., <strong>\u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"31\">\n<li>Kocaba\u015f, P., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"30\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Yilg\u00f6r, 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<\/li>\n<\/ol>\n<ol start=\"29\">\n<li>Ileri, N., <strong>\u00c7al\u0131k, P<\/strong>. Effects of pH strategy on endo- and exo-metabolome profiles and sodium potassium hydrogen ports of \u03b2-lactamase-producing Bacillus licheniformis (2006) Biotechnology Progress, 22 (2), pp. 411-419.<\/li>\n<\/ol>\n<ol start=\"28\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Ileri, N., Erdin\u00e7, B.I., Aydogan, N., Argun, M. Novel antifoam for fermentation processes: Fluorocarbon-hydrocarbon hybrid unsymmetrical bolaform surfactant (2005) Langmuir, 21 (19), pp. 8613-8619.<\/li>\n<\/ol>\n<ol start=\"27\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Arifo\u01e7lu, M., \u00c7al\u0131k, G. Oxygen transfer effects in \u03b2-lactamase fermentation by Bacillus licheniformis in a glucose-based defined medium (2005) Journal of Chemical Technology and Biotechnology, 80 (9), pp. 1062-1071.<\/li>\n<\/ol>\n<ol start=\"26\">\n<li>\u00d6z\u00e7elik, I.\u015e., <strong>\u00c7al\u0131k, P.<\/strong>, \u00c7al\u0131k, G., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"25\">\n<li>\u00c7al\u0131k, G., Pehlivan, N., \u00d6z\u00e7elik, I.\u015e., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"24\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Yilg\u00f6r, P., Ayhan, P., Demir, A.S. Oxygen transfer effects on recombinant benzaldehyde lyase production (2004) Chemical Engineering Science, 59 (22-23), pp. 5075-5083.<\/li>\n<\/ol>\n<ol start=\"23\">\n<li>\u00c7elik, E., <strong>\u00c7al\u0131k, P.<\/strong> Bioprocess parameters and oxygen transfer characteristics in \u03b2-lactamase production by Bacillus species (2004) Biotechnology Progress, 20 (2), pp. 491-499.<\/li>\n<\/ol>\n<ol start=\"22\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Bilir, E., \u00d6z\u00e7elik, I.\u015e., \u00c7al\u0131k, G., \u00d6zdamar, T.H. Inorganic compounds have dual effect on recombinant protein production: Influence of anions and cations on serine alkaline protease production\u00a0(2004) Journal of Applied Microbiology, 96 (1), pp. 194-200.<\/li>\n<\/ol>\n<ol start=\"21\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Kalender, N., \u00d6zdamar, T.H. Overexpression of serine alkaline protease encoding gene in Bacillus species: Performance analyses (2003) Enzyme and Microbial Technology, 33 (7), pp. 967-974.<\/li>\n<\/ol>\n<ol start=\"20\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00c7elik, E., Telli, I.E., Oktar, C., \u00d6zdemir, E. Protein-based complex medium design for recombinant serine alkaline protease production (2003) Enzyme and Microbial Technology, 33 (7), pp. 975-986.<\/li>\n<\/ol>\n<ol start=\"19\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Tomlin, G.C., Oliver, S.G., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"18\">\n<li>\u00c7al\u0131k, G., Pehlivan, N., Kalender, N., \u00d6zdamar, T.H., <strong>\u00c7al\u0131k, P. <\/strong>Utilization of pretreated molasses for serine alkaline protease production with recombinant Bacillus species (2003) Chemical Engineering Communications, 190 (5-8), pp. 630-644.<\/li>\n<\/ol>\n<ol start=\"17\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Bayram, A., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"16\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Bilir, E., \u00c7al\u0131k, G., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"15\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u015eenver \u00d6z\u00e7elik, I., \u00c7al\u0131k, G., \u00d6zdamar, T.H. Enzyme-ion exchanger interactions in serine alkaline protease separation: Theory, equilibria and kinetics (2002) Biochemical Engineering Journal, 12 (3), pp. 193-204.<\/li>\n<\/ol>\n<ol start=\"14\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Bilir, E., \u00c7al\u0131k, G., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"13\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, T.H. Bioreaction network flux analysis for industrial microorganisms: A review\u00a0(2002) Reviews in Chemical Engineering, 18 (6), pp. 553-596.<\/li>\n<\/ol>\n<ol start=\"12\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"11\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00c7al\u0131k, G., \u00d6zdamar, T.H. Bioprocess development for serine alkaline protease production: A review (2001) Reviews in Chemical Engineering, 17 (4 SUPPL.), pp. 1-59.<\/li>\n<\/ol>\n<ol start=\"10\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, T.H. Carbon sources affect metabolic capacities of Bacillus species for the production of industrial enzymes: Theoretical analyses for serine and neutral proteases and \u03b1-amylase (2001) Biochemical Engineering Journal, 8 (1), pp. 61-81.<\/li>\n<\/ol>\n<ol start=\"9\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00c7al\u0131k, G., Taka\u00e7, S., \u00d6zdamar, T.H. Metabolic flux analyses for serine alkaline protease production (2000) Enzyme and Microbial Technology, 27 (10), pp. 793-805.<\/li>\n<\/ol>\n<ol start=\"8\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00c7al\u0131k, G., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"7\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, 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.<\/li>\n<\/ol>\n<ol start=\"6\">\n<li>Taka\u00e7, S., Elmas, S., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"5\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, Taka\u00e7, S., \u00c7al\u0131k, G., \u00d6zdamar, T.H. Serine alkaline protease overproduction capacity of Bacillus licheniformis (2000) Enzyme and Microbial Technology, 26 (1), pp. 45-60.<\/li>\n<\/ol>\n<ol start=\"4\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00c7al\u0131k, G., Taka\u00e7, S., \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"3\">\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, 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.<\/li>\n<\/ol>\n<ol start=\"2\">\n<li>\u00c7al\u0131k, G., Sava\u015f\u00e7i, H., <strong>\u00c7al\u0131k, P.<\/strong>, \u00d6zdamar, T.H. Growth and \u03ba-carrageenan immobilization of Pseudomonas dacunhae cells for L-alanine production (1999) Enzyme and Microbial Technology, 24 (1-2), pp. 67-74.<\/li>\n<\/ol>\n<ol>\n<li><strong> \u00c7al\u0131k, P.<\/strong>, \u00c7al\u00edk, G., \u00d6zdamar, 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.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>PATENTS \u00c7al\u0131k P., Erg\u00fcn B.G., 1.07.2025. \u2018\u2019Modified AOX1 Promoter Variants\u2019\u2019 Publication number: WO\/2020\/068018, US12344848B2. . \u00c7al\u0131k P., Erg\u00fcn B.G., 17.09.2024. \u2018\u2019Design of Alcohol Dehydrogenase 2 (ADH2) Promoter Variants by Promotor Engineering\u2019\u2019, US12091658B2. SCI PUBLICATIONS 95. Wei Xigang, Cong Wenjie, Zhou Hualan, Zhang Jianguo, \u00c7al\u0131k P., 2026. Decode and Rewire: Programming Komagataella phaffii for Bioproduction with [&hellip;]<\/p>\n","protected":false},"author":4302,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-8","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/blog.metu.edu.tr\/indbio\/wp-json\/wp\/v2\/pages\/8","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blog.metu.edu.tr\/indbio\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blog.metu.edu.tr\/indbio\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blog.metu.edu.tr\/indbio\/wp-json\/wp\/v2\/users\/4302"}],"replies":[{"embeddable":true,"href":"https:\/\/blog.metu.edu.tr\/indbio\/wp-json\/wp\/v2\/comments?post=8"}],"version-history":[{"count":0,"href":"https:\/\/blog.metu.edu.tr\/indbio\/wp-json\/wp\/v2\/pages\/8\/revisions"}],"wp:attachment":[{"href":"https:\/\/blog.metu.edu.tr\/indbio\/wp-json\/wp\/v2\/media?parent=8"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}