Academic Publications

Published or accepted to be published in journals covered by SCI, SSCI or AHCI

International

• Başak Özay , Ezgi Yağmur Tükel , Gizem Ayna Duran and Yağmur Kiraz.
  (2024) Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening.
  Analytical Biochemisty , Vol. 694, No. 115619,

• Garavis Miguel , Patrick Edwards , Israel Serrano-Chacon , Osman Doluca , Vyacheslav Filichev and Carlos Gonzales.
  (2024) Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex.
  Nucleic Acid Research , Vol. 52, No. 5,

• Gizem Duran.
  (2023) Pan-cancer analyses identifies the RRM2 gene as a biomarker with diagnostic and prognostic roles in multiple human cancers via interacting with the hsa-let-7a-5p miRNA and EZH2.
  Journal Of Biological Regulators And Homeostatic Agents , Vol. 37, No. 11,

• İlayda Akaçin , Şeymanur Ersoy , Osman Doluca , Mine Güngörmüşler.
  (2023) Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH2 production.
  Scientific Reports , No. 13,

• Gizem Duran , Fatma Sert.
  (2023) Determination of Eight Hub Genes and Functional Pathways Affecting both the Survival of Early- and Late-Stage Colon Cancer Patients.
  Turkish Journal Of Oncology , Vol. 38, No. 4,

• Arıkan Ayşe , Osman Doluca , Sıla Akhan , Tamer Şanlıdağ , Murat Sayan.
  (2023) Evaluation of lateral flow and ELISA techniques for detecting IgG and IgM antibodies in COVID-19 cases in Turkiye.
  Eastern Mediterranean Health Journal , Vol. 29, No. 2,

• İlayda Akaçin , Şeymanur Ersoy , Osman Doluca , Mine Güngörmüşler.
  (2022) Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics.
  Microbiological Research ,

• Hakan Ünver , Burak Berber , Beyza Kanat , Mahmoud Arafat , Ayşe Tansu Koparal and Osman Doluca.
  (2022) DNA binding effects of 2,2′-bipyridine and 1,10-phenanthroline ligands synthesized with benzimidazole copper (II) complexes: Crystal structure, molecular docking, DNA binding and anti-cancer studies.
  Polyhedron , Vol. 221,

• Gizem Duran , Yasemin Bendeli Cihan.
  (2022) Autophagy-related genes affect the survival of multiple myeloma patients depending on chromosomal abnormality.
  Asian Biomedicine , Vol. 16, No. 5,

• Osman Doluca , Kaya Oğuz.
  (2021) APAL: Adjacency Propagation Algorithm for Overlapping Community Detection in Biological Networks.
  Information Sciences , Vol. 579, 574-590,

• Hüseyin Saygın Portakal , Beyza Kanat , Murat Sayan , Burak Berber , Osman Doluca.
  (2021) A novel method for conserved sequence extraction with prospective mutation prediction for SARS-CoV-2 PCR primer design.
  Journal Of Virological Methods , Vol. 1, No. 293, 1-8, ISBN: 114146

• Halil Duyar , Hüseyin Saygın Portakal , Ergin Yalçın , Beyza Kanat , Osman Doluca.
  (2021) Fluorene/fluorenone carboxamide derivatives as selective light-up fluorophores for c-myc G-quadruplex.
  Bioorganic & Medicinal Chemistry Letters , Vol. 36, No. 127824,

• Burak Berber , Osman Doluca.
  (2021) A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin–dopamine receptors.
  Briefings In Bioinformatics , Vol. 22, No. 2,

• Yahya Nural , Sadin Ozdemir , Osman Doluca , Bunyamin Demir , Mustafa Serkan Yalcin , Hasan Atabey , Beyza Kanat , Selma Erat , Hayati Sari and Zeynel Seferoglu.
  (2020) Synthesis, biological properties, and acid dissociation constant of novel naphthoquinone–triazole hybrids.
  Bioorganic Chemistry , Vol. 105,

• Ayse Arikan , Murat Sayan , Osman Doluca , Osman Doluca.
  (2020) NeuMoDx random access molecular diagnostic system for detection and quantification of hepatitis B virus in clinical samples.
  The Journal Of Infection In Developing Countries , Vol. 14, No. 10, 1197-1203,

• Meryem Chemchem , Issah Yahaya , Burcu Aydıner , Osman Doluca , Nurgül Seferoğlu , Zeynel Seferoğlu.
  (2020) Substituent dependent selectivity of fluorescent chemosensors derived from coumarin for biologically relevant DNA structures and anions.
  Sensors And Actuators B: Chemical , Vol. 305, No. 15,

• Figen Sarıgül , Osman Doluca , Murat Sayan.
  (2020) Investigation of Compatibility of SARS-CoV-2 RT-PCR Kits Containing Different Gene Targets During COVID-19 Pandemic.
  Future Virology , Vol. 15, No. 8, 515-524,

• Osman Doluca.
  (2019) G-Quadruplex enrichment analysis reveals their role as intronic regulatory elements in plants.
  Turkish Journal Of Botany , Vol. 43, 151-166,

• Meryem Chemchem , Issah Yahaya , Burcu Aydıner , Nurgül Seferoğlu , Osman Doluca , Naima Merabet , Zeynel Seferoğlu.
  (2018) A novel and synthetically facile coumarin-thiophene-derived Schiff base for selective fluorescent detection of cyanide anions in aqueous solution: synthesis, anion interactions, theoretical study and DNA-binding properties.
  Tetrahedron , Vol. 74, No. 48, 6897-6906,

• Yalçın Kılıç , Serkan Bolat , İbrahim KANİ.
  (2018) A carboxylate-bridged Mn(II) compound with 6-methylanthranilate/bipy: oxidation of alcohols/alkenes and catalase-like activity, Journal of Coordination Chemistry 71 (2018)..
  Journal Of Coordination Chemistry , Vol. 71,

• Yalçın Kiliç , İbrahim Kani.
  (2017) Selective Catalytic Oxidation of Alkenes Employing Homobinuclear Manganese(II) Catalysts with TBHP.
  Polyhedron, Volume 141, 15 February 2018, Pages 352-359 ,

• Oktay Kaplan , Burak Berber , Nezih Hekim , Osman Doluca.
  (2016) G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.
  Nucleic Acid Research , Vol. 44,

• Osman Doluca , Jamie Withers , Trevor Loo , Patrick Edwards , Carlos Gonzalez , Vyacheslav Filichev.
  (2015) Interdependence of pyrene interactions and tetramolecular G4-DNA assembly.
  Organic & Biomolecular Chemistry , Vol. 13, No. 12, 3742-3748,

• Begüm Alural , Gizem Ayna Duran , Kemal Uğur Tüfekçi , Jens Allmer , Zeynep Önkal , Doğan Tunalı , Kürşad Genç , Şermin Genç.
  (2014) EPO mediates neurotrophic, neuroprotective, anti-oxidant, and anti-apoptotic effects via downregulation of miR-451 and miR-885-5p in SH-SY5Y neuron-like cells.
  Frontiers In Immunology , Vol. 5, No. 475,

• Okan Zafer Yeşilel , Yalçın Kılıç , Onur Şahin , Orhan Büyükgüngör.
  (2014) One-dimensional coordination polymers of copper(II), cobalt(II), zinc(II) and cadmium(II) with glutarate and N-methylimidazole.
  Polyhedron , Vol. 67, No. 8, 122-128, ISBN: 0277-5387

• Osman Doluca , Tracy Hale , Patrick Edwards , Carlos Gonzalez , Vyacheslav Filichev.
  (2014) Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence‐Specific Detection of Double‐Stranded DNA.
  ChemPlusChem , Vol. 79, No. 1, 58-66,

• Osman Doluca , Jamie Withers , Vyacheslav Filichev.
  (2013) Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes.
  Chemical Reviews , Vol. 113, No. 5, 3044-3083,

• Murat Taş , Seval Çamur , Yalçın Kılıç , Hakan Dal.
  (2012) The two Bis(4-aminosalicylato-O) bis(N,N-dimethylethylenediamine)Ni(II) complexes.
  Zeitschrift Für Kristallographie - Crystalline Materials , Vol. 227, 837-842, ISBN: 2012

• Gizem Ayna Duran , Dmitri Krysko , Aga Kaczmarek , Goran Petrovski , Peter Vandenabeele , Laszlo Fesus.
  (2012) ATP release from dying autophagic cells and their phagocytosis are crucial for inflammasome activation in macrophages.
  PLOS ONE , Vol. 7, No. 6, e40069,

• Goran Petrovski , Gizem Ayna Duran , Gyöngyike Májai , Judit Hodrea , Szilvia Benkő , András Mádi , László Fésüs.
  (2011) Phagocytosis of cells dying through autophagy induces inflammasome activation and IL-1β release in human macrophages.
  Autophagy , No. 7, ISBN: 3

• Murat Taş , Seval Çamur , Yalçın Kılıç.
  (2011) The synthesis and characterization of copper(II)–p-aminosalicylate complexes with diamine ligands.
  Journal Of Thermal Analysis And Calorimetry , Vol. 103, No. 3, 995-1000, ISBN: 1588-2926

• Alexandre Boutorine , Osman Doluca , Vyacheslav Filichev.
  (2009) Optimization of the sequence of twisted intercalating nucleic acids (TINA) forming triple helix with the polypurine tract of the proviral HIV DNA.
  Nucleic Acids Symp Series , Vol. 53, No. 1, 139-140,

• Osman Doluca , Emel Ordu , Halil Kısakesen , Richard Sessions , A Clarke , Candan Tamerler , Nevin Karagüler.
  (2008) Effects of cysteine/cystine engineering on thermal stability of formate dehydrogenase from Candida methylica.
  FEBS JOURNAL , Vol. 275, 398-398,

Published or accepted to be published in journals covered by other indexes

National

• Gizem Ayna Duran.
  (2024) Kolanjiyokarsinom ve Hepatoselüler Karsinom Hastalarında Farklı Genler Tarafından Tetiklenen Ortak Biyolojik Yolaklar.
  Manisa Celal Bayar Sağlık Bilimleri Enstitüsü Dergisi , Vol. 11, No. 1, 141-149,

International

• Duygu Geçkin , Güleser Kalaycı Demir.
  (2024) Siamese Neural Networks Based Ensemble Model for the Prediction of Protein-Protein Interactions.
  Karaelmas Science And Engineering Journal , Vol. 14, No. 2,

• Gizem Ayna Duran.
  (2024) Circulating tumour cells differentially express upregulated cancer biomarkers “lncRNAs and miRNAs” compared to bone marrow biopsy samples in multiple myeloma patients.
  Journal Of Experimental And Clinical Medicine , Vol. 2, No. 41, 351-360,

• Gizem Duran.
  (2024) Upregulated Acute Systemic Inflammation Related Genes based on Endotoxin Exposure Provide “Survival Benefit” or Create “High Risk of Death” in Leukemia and Colon Cancer Patients.
  European Journal Of Biology ,

• Cansu Ergun , Buse Zeren Kiremitci , Gizem Arslantaş , Busenur Bozkurt , Gizem Ayna Duran , Yağmur Kiraz.
  (2023) Novel Drug Candidates Targeting PI3K Pathway in Acute Myeloid Leukemia Treatment.
  Experimed ,

• Osman Doluca.
  (2019) Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability.
  Hittite Journal Of Science And Engineering , Vol. 6, No. 4, 303-308,