Publications

Recent Publications:

  • Akgul R, Morgil H, Kizilkaya IT, Sarayloo E, Cevahir G, Akgul F, Kavakli IH (2022) Transcriptomic and fatty acid analyses of Neochloris aquatica grown under different nitrogen concentration. Funct Integr Genomics 22:407-421.
  • Cakilkaya B, Kavakli IH, DeMirci H (2022) The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region. J Biol Chem 299:102794.
  • Gul H, Selvi S, Yilmaz F, Ozcelik G, Olfaz-Aslan S, Yazan S, Tiryaki B, Gul S, Yurtseven A, Kavakli IH, Ozlu N, Ozturk N (2022) Proteome analysis of the circadian clock protein PERIOD2. Proteins 90:1315-1330.
  • Gul S, Akyel YK, Gul ZM, Isin S, Ozcan O, Korkmaz T, Selvi S, Danis I, Ipek OS, Aygenli F, Taskin AC, Akarlar BA, Ozlu N, Ozturk N, Ozturk N, Ünal D, Guzel M, Turkay M, Okyar A, Kavakli IH (2022) Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice. Nat Commun 13:6742.
  • Gul S, Kavakli IH (2022) The Structure-Based Molecular-Docking Screen Against Core Clock Proteins to Identify Small Molecules to Modulate the Circadian Clock. In: Solanas G, Welz PS (eds) Circadian Regulation: Methods and Protocols. Springer US New York, NY, pp. 15-34.
  • Kavakli IH, Gul S, Turkay M (2022) Identification of novel small molecules targeting core clock proteins to regulate circadian rhythm. Curr Opin Chem Eng 35:100730.
  • Kavakli IH, Ozturk N, Baris I (2022) Protein interaction networks of the mammalian core clock proteins. In: Donev R (ed) Advances in Protein Chemistry and Structural Biology. Academic Press, pp. 207-233.
  • Parlak GC, Camur BB, Gul S, Ozcan O, Baris I, Kavakli IH (2022) The secondary pocket of cryptochrome 2 is important for the regulation of its stability and localization. Journal of Biological Chemistry 298:102334.
  • Cal-Kayitmazbatir S, Kulkoyluoglu-Cotul E, Growe J, Selby CP, Rhoades SD, Malik D, Oner H, Asimgil H, Francey LJ, Sancar A, Kruger WD, Hogenesch JB, Weljie A, Anafi RC, Kavakli IH (2021) CRY1-CBS binding regulates circadian clock function and metabolism. FEBS J 288:614-639.
  • Emisoglu-Kulahli H, Gul S, Morgil H, Ozcan O, Aygenli F, Selvi S, Kavakli IH, Ozturk N (2021) Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects. Funct Integr Genomics 21:1-16.
  • Gul S, Ozcan O, Asar S, Okyar A, Barıs I, Kavakli IH (2021) In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials. Journal of Biomolecular Structure and Dynamics 39:6772-6791.
  • Gul S, Rahim F, Isin S, Yilmaz F, Ozturk N, Turkay M, Kavakli IH (2021) Structure-based design and classifications of small molecules regulating the circadian rhythm period. Scientific Reports 11:18510.
  • Karatum O, Aria MM, Eren GO, Yildiz E, Melikov R, Srivastava SB, Surme S, Dogru IB, Bahmani Jalali H, Ulgut B, Sahin A, Kavakli IH, Nizamoglu S (2021) Nanoengineering InP Quantum Dot-Based Photoactive Biointerfaces for Optical Control of Neurons. Front Neurosci 15:652608.
  • Ozcan O, Gul S, Kavakli IH (2021) Allosteric Regulation of CRYs in Mammalian Circadian Clock. Computer Aided Chemical Engineering. Elsevier, pp. 2025-2031.
  • Srivastava SB, Melikov R, Yildiz E, Dikbas UM, Sadeghi S, Kavakli IH, Sahin A, Nizamoglu S (2021) Bulk-heterojunction photocapacitors with high open-circuit voltage for low light intensity photostimulation of neurons. J Mater Chem C 9:1755-1763.
  • Organic Photovoltaic Pseudocapacitors for Neurostimulation;Han M, Srivastava SB, Yildiz E, Melikov R, Surme S, Dogru-Yuksel IB, Kavakli IH, Sahin A, Nizamoglu S. ACS Appl Mater Interfaces.  2020 Sep 8. doi: 10.1021/acsami.0c11581.

  • Plasmon-Coupled Photocapacitor Neuromodulators;Melikov R, Srivastava SB, Karatum O, Dogru-Yuksel IB, Bahmani Jalali H, Sadeghi S, Dikbas UM, Ulgut B, Kavakli IH, Cetin AE, Nizamoglu S. ACS Appl Mater Interfaces. 2020 Aug 12;12(32):35940-35949.

  • New Biocompatible Antibacterial Wound Dressing Candidates; Agar-Locust Bean Gum and Agar-Salep Films. Akkaya NE, Ergun C, Saygun A, Yesilcubuk N, Akel-Sadoglu N, Kavakli IH, Turkmen HS, Catalgil-Giz H. Int J Biol Macromol. 2020, 15;155:430-438.

  • Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling. Muratcioglu S, Aydin C, Odabasi E, Ozdemir ES, Firat-Karalar EN, Jang H, Tsai CJ, Nussinov R,Kavakli IH, Gursoy A, Keskin O. J Mol Biol. 2020,14;432(4):1199-1215.
  • Identification and Characterization of a New Class of (6-4) Photolyase From Vibrio cholerae. Dikbas UM, Tardu M, Canturk A, Gul S, Ozcelik G, Baris I, Ozturk N, and Kavakli IH. Biochemistry. 2019, 58(43):4352-4360
  • Biocompatible Quantum Funnels for Neural Photostimulation. Bahmani Jalali H, Karatum O, Melikov R, Dikbas UM, Sadeghi S, Yildiz E, Dogru IB, Ozgun Eren G, Ergun C, Sahin A, Kavakli IH, Nizamoglu S.  Nano Letter, 2019, 19(9):5975-5981.  doi: 10.1021/acs.nanolett.9b01697.
  • Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits. Hande Morgil, Mehmet Tardu, Gül Cevahir, İbrahim Halil Kavakli. Functional & Integrative Genomics, 2019, 19:715-727
  • Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level.  Cavga AD, Tardu M,  Korkmaz T,  Keskin O, Ozturk N, Gursoy A, Kavakli IH.  Functional & Integrative Genomics, 2019, 19:729-742
  • Band Alignment Engineers Faradaic and Capacitive Photostimulation of Neurons Without Surface Modification;Shashi Bhushan Srivastava, Rustamzhon Melikov, Mohammad Mohammadi Aria, Ugur Meric Dikbas, Ibrahim Halil Kavakli, Sedat Nizamoglu. Physical Review Applied. 11, 044012.doi.org/10.1103/PhysRevApplied.11.044012
  • Perovskite‐Based Optoelectronic Biointerfaces for Non‐Bias‐Assisted Photostimulation of Cells.Mohammad M. Aria, Shashi B. Srivastava, Emine Sekerdag, Ugur M. Dikbas, Sadra Sadeghi, Samuel R. Pering, Petra J. Cameron, Yasemin Gursoy-Ozdemir, Ibrahim H. Kavakli, and Sedat Nizamoglu. Advanced Materials Interfaces, 2019, e1900758, DOI:10.1002/admi.201900758
  • Centriolar satellites are required for efficient ciliogenesis and ciliary content regulation.  Ezgi Odabasi, Seref Gul, Ibrahim H Kavakli, and Elif N Firat-Karalar. EMBO Reports, 2019, 20(6):e47723, DOI 10.15252/embr.201947723
  • DNA repair by photolyases Ibrahim Halil Kavakli, Nuri Ozturk Seref Gul. Adv Protein Chem Struct Biol, 2019, 115:1-19, DOI: 10.1016/bs.apcsb.2018.10.003
  • Effective Neural Photostimulation Using Indium-Based Type-II Quantum Dots.Houman Bahmani Jalali, Mohammad Mohammadi Aria, Ugur Meric Dikbas, Sadra Sadeghi, Baskaran Ganesh Kumar, Mehmet Sahin, Ibrahim Halil Kavakli, Cleva W. Ow-Yang, and Sedat Nizamoglu. ACS Nano, 2018, 12 (8), 8104-8114 DOI: 10.1021/acsnano.8b02976.
  • Upgrading blends of microalgae feedstocks and heavy oils in supercritical water.
    Ramazan Oguz Caniaz, Salim Simsek, Serhat Arca, Ehsan Sarayloo, Ibrahim Halil Kavakli, Can Erkey. The Journal of Supercritical Fluids, 2018, 133 (2), 674-682. DOI: 10.1016/j.supflu.2017.09.002.
  • Enhancement of the lipid productivity and fatty acid methyl ester profile of Chlorella vulgaris by two rounds of mutagenesis.
    Ehsan Sarayloo, Salim Simsek, Yigit Sabri Unlu, Gul Cevahir, Can Erkey, Ibrahim Halil Kavakli. Bioresource Technology, 2018 250, 764-769. DOI: 10.1016/j.biortech.2017.11.105.
  • Understanding lipid metabolism in high-lipid-producing Chlorella vulgaris mutants at the genome-wide level
    Ehsan Sarayloo, Mehmet Tardu, Yigit Sabri Unlu, Salim Simsek, Gul Cevahir, Can Erkey, Ibrahim Halil Kavakli. Algal Research, 2017 28, 244-252. DOI: 10.1016/j.algal.2017.11.009
  • Molecular aspects of circadian pharmacology and relevance for cancer chronotherapy
    Narin Ozturk, Dilek Ozturk, Ibrahim Halil Kavakli, Alper Okyar. Int. J. Mol. Sci. 2017, 18(10), 2168. DOI: 10.3390/ijms18102168
  • Day-Time Isoflurane Administration Suppresses Circadian Gene Expressions in Both the Brain and a Peripheral Organ, Liver.
    Necati Gökmen, İbrahim Barış, Elvan Öçmen, Osman Yılmaz, Ali Günerli, İbrahim Halil Kavaklı.Turk J Anaesthesiol Reanim. 2017 Aug; 45(4): 197–202. DOI: 10.5152/TJAR.2017.68466
  • Clock regulation of metabolites reveals coupling between transcription and metabolism.
    Saikumari Y Krishnaiah, Gang Wu, Brian J Altman, Jacqueline Growe, Seth D Rhoades, Faith Coldren, Anand Venkataraman, Anthony O Olarerin-George, Lauren J Francey, Sarmistha Mukherjee, Saiveda Girish, Christopher P Selby, Sibel Cal, ER Ubeydullah, Bahareh Sianati, Arjun Sengupta, Ron C Anafi, I Halil Kavakli, Aziz Sancar, Joseph A Baur, Chi V Dang, John B Hogenesch, Aalim M Weljie. Cell Metabolism, 2017, 25(4), 961-974. DOI: 10.1016/j.cmet.2017.03.019
  • MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae.
    Mehmet Tardu, Selma Bulut, Ibrahim Halil Kavakli. Scientific Reports, 2017, 7,  40817.  DOI: 10.1038/srep40817
  • The photolyase/cryptochrome family of proteins as DNA repair enzymes and transcriptional repressors
    Ibrahim Halil Kavakli, Ibrahim Baris, Mehmet Tardu, Şeref Gül, Haşimcan Öner, Sibel Çal, Selma Bulut, Darya Yarparvar, Çağlar Berkel, Pınar Ustaoğlu, Cihan Aydın. Photochemistry and Photobiology, 2017, 93 ,93–103.
    DOI: 10.1111/php.12669
  • RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae
    Mehmet Tardu, Ugur Meric Dikbas, Ibrahim Baris, Ibrahim Halil Kavakli. Functional & Integrative Genomics, 2018, 16(6), 657-669. DOI:  10.1007/s10142-016-0521-0
  • Glu-370 in the large subunit influences the substrate binding, allosteric, and heat stability properties of potato ADP-glucose pyrophosphorylase.
    Ayse Bengisu Seferoglu, Seref Gul, Ugur Meric Dikbas, Ibrahim Baris, Kaan Koper, Mahmut Caliskan, Gul Cevahir. Plant Science, 2016, 252, 125-132. DOI: 10.1016/j.plantsci.2016.07.007.
  • Reduced glucose sensation can increase the fitness of Saccharomyces cerevisiae lacking mitochondrial DNA
    Emel Akdogan, Mehmet Tardu, Gorkem Garipler, Gulkiz Baytek, I Halil Kavakli, Cory C Dunn. Plos One , 2016, 11(1):e0146511. doi: 10.1371/journal.pone.0146511
  • Glu-370 in the large subunit influences the substrate binding, allosteric, and heat stability properties of potato ADP-glucose pyrophosphorylaseAyse Bengisu Seferoglu, Seref Gul, Ugur Meric Dikbas, Ibrahim Baris, Kaan Koper, Mahmut Caliskan, Gul Cevahir. Plant Science, 2016, 252, 125-132. DOI: 10.1016/j.plantsci.2016.07.007.
  • A novel BHLHE41 variant is associated with short sleep and resistance to sleep deprivation in humansPellegrino R, Kavakli IH, Goel N, Cardinale CJ, Dinges DF, Kuna ST, Maislin G, Van Dongen HP, Tufik S, Hogenesch JB, Hakonarson H, Pack AI. Sleep  , 2014, 37(8):1327-36. doi: 10.5665/sleep.3924
  • Enhanced heterotetrameric assembly of potato ADP-glucose pyrophosphorylase using reverse genetics
    Seferoglu AB, Koper K, Can FB, Cevahir G, Kavakli IH. Plant Cell Physiol. 2014, 55(8):1473-83. doi: 10.1093/pcp/pcu078
  • Machine learning helps identify CHRONO as a circadian clock component
    Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. PLoS Biol, 2014, 15(6):R86. doi: 10.1186/gb-2014-15-6-r86
  • IVT-seq reveals extreme bias in RNA sequencing
    Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. Genome Biol, 2014, 12(4):e1001840. doi: 10.1371/journal.pbio.1001840

All Publications:

PubMed