• Emerging DNA Methylome Targets in FLT3-ITD-Positive Acute Myeloid Leukemia: Combination Therapy with Clinically Approved FLT3 Inhibitors 

  Tecik, Melisa; Adan, Aysun (SPRINGER LINK, 2024)

  The internal tandem duplication (ITD) mutation of the FMS-like receptor tyrosine kinase 3 (FLT3-ITD) is the most common mutation observed in approximately 30% of acute myeloid leukemia (AML) patients. It represents poor ...

• Draft genome of carotenoid-producing endophytic Pseudomonas sp. 102515 from Taxus chinensis 

  Fidan, Ozkan (American Society for Microbiology, 2024)

  Here, we report the draft genome sequence of endophytic Pseudomonas sp. 102515 isolated from Taxus chinensis collected from Logan, UT, USA. The genome is composed of 36 contigs and around 4.9 Mbp in size. The GC content ...

• Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM 

  Madsen, Jesper J.; Ohkubo, Y. Zenmei (Public Library of Science, 2024)

  Membrane binding is a crucial mechanism for many proteins, but understanding the specific interactions between proteins and membranes remains a challenging endeavor. Coagulation factor Va (FVa) is a large protein whose ...

• CilioGenics: an integrated method and database for predicting novel ciliary genes 

  Pir, Mustafa Samet; Begar, Efe; Yenisert, Ferhan; Demirci, Hasan C.; Korkmaz, Mustafa E.; Karaman, Asli; Tsiropoulou, Sofia; Firat-Karalar, Elif Nur; Blacque, Oliver E.; Oner, Sukru S.; Doluca, Osman; Cevik, Sebiha; Kaplan, Oktay Ismail (Oxford University Press, 2024)

  Uncovering the full list of human ciliary genes holds enormous promise for the diagnosis of cilia-related human diseases, collectively known as ciliopathies. Currently, genetic diagnoses of many ciliopathies remain incomplete ...

• Amelioration potential of synthetic oxime chemical cores against multiple sclerosis and Alzheimer's diseases: Evaluation in aspects of in silico and in vitro experiments 

  Yilmaz, Anil; Koca, Murat; Ercan, Selami; Acar, Ozden Ozgun; Boga, Mehmet; Sen, Alaattin; Kurt, Adnan (ELSEVIER, 2024)

  Alzheimer disease (AD) and multiple sclerosis (MS) are inflammatory neurological disorders. The main symptom of AD is dementia, and the main symptoms of MS are vertigo, sexual dysfunction, cognitive problems, and fatigue. ...

• Investigating the Impact of Birt–Hogg–Dubé Syndrome Associated Folliculin (FLCN) and Retinitis Pigmentosa 2 (RP2) Loss on Cilia Function and Morphology 

  Kaplan, Oktay İsmail (Cumhuriyet Üniversitesi, 2024)

  Folliculin (FLCN), a GTPase-activating protein (GAP), has been linked to Birt–Hogg–Dubé syndrome, the mTORC1 signaling pathway and cilia. Disruptions in cilia structure and function lead to a group of diseases known as ...

• Computational Detection of Pre-microRNAs 

  Saçar Demirci, Müşerref Duygu (Humana Press Inc., 2022)

  MicroRNA (miRNA) studies have been one of the most popular research areas in recent years. Although thousands of miRNAs have been detected in several species, the majority remains unidentified. Thus, finding novel miRNAs ...

• Integrative analyses in omics data: Machine learning perspective 

  Yazici, Miray Unlu; Bakir-Gungor, Burcu; Yousef, Malik (Deutsche Gesellschaft fur Medizinische Informatik, Biometrie und Epidemiologie e.V., 2023)

  Developments in the high throughput technologies have enabled the production of an immense amount of knowledge at the multi-omics level. Considering complex diseases which are affected by multi-factors, single omics datasets ...

• Isothiocyanates as drug candidates in cancer prevention and treatment 

  Saylan, Demet; Cebeci, Fatma (IGI Global, 2023)

  Cancer is the second most common cause of death worldwide. Many methods such as surgery, chemotherapy, radiation therapy, etc. are being used for treatment. Most patients have a combination treatment with chemotherapy along ...

• In silico Evaluation of the Potential of Natural Products from Chili Pepper as Antiviral Agents Against Dna-Directed Rna Polymerase of the Monkeypox Virus 

  Fidan, Özkan; Mujwar, Somdutt (Bitlis Eren Üniversitesi, 2024)

  This study focused on the discovery of new drug candidates effective against the monkeypox virus. Virtual screening was performed to evaluate the potential of chili pepper natural products against homology-modeled DNA-directed ...

• Pleiotropic molecular effects of dietary polyphenols resveratrol and apigenin in Leukemia 

  Adan, Aysun; Oğuz, Osman (ELSEVIER, 2018)

  Resveratrol and apigenin are commonly found polyphenols in many fruits and vegetables and recognition of these dietary polyphenols for human health owing to their biological and pharmacological features including ...

• MSABrowser: dynamic and fast visualization of sequence alignments, variations and annotations 

  Torun, Furkan M.; Bilgin, Halil İbrahim; Kaplan, Oktay I. (Oxford University Press, 2021)

  Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, ...

• Identifying Taxonomic Biomarkers of Colorectal Cancer in Human Intestinal Microbiota Using Multiple Feature Selection Methods 

  Jabeer, Amhar; Kocak, Aysegul; Akkas, Huseyin; Yenisert, Ferhan; Nalbantoglu, Ozkan Ufuk; Yousef, Malik; Bakir Gungor, Burcu (Institute of Electrical and Electronics Engineers Inc., 2022)

  A variety of bacterial species called gut microbiota work together to maintain a steady intestinal environment. The gastrointestinal tract contains tremendous amount of different species including archaea, bacteria, fungi, ...

• Therapeutic Targeting of FLT3 in Acute Myeloid Leukemia: Current Status and Novel Approaches 

  Tecik, Melisa; Adan, Aysun (Dove Medical Press Ltd, 2022)

  FMS-like tyrosine kinase 3 (FLT3) is mutated in approximately 30% of acute myeloid leukemia (AML) patients. The presence of FLT3-ITD (internal tandem duplication, 20–25%) mutation and, to a lesser extent, FLT3-TKD (tyrosine ...

• Cerium Oxide Nanoparticles Biosynthesized Using Fresh Green Walnut Shell in Microwave Environment and their Anticancer Effect on Breast Cancer Cells 

  Sulak, Mine; Turgut, Gurbet Celik; Sen, Alaattin (John Wiley and Sons Inc, 2022)

  In this study, cerium oxide nanoparticles (CONPs) were synthesized using fresh green walnut shell extract in microwave environment. The morphology and structure of the CONPs were determined using ultraviolet-visible (UV/VIS), ...

• Evaluation of Anti-Alzheimer Activity of Synthetic Coumarins by Combination of in Vitro and in Silico Approaches 

  Erdogan Orhan, Ilkay; Deniz, F. Sezer Senol; Salmas, Ramin Ekhteiari; Irmak, Sule; Acar, Ozden Ozgun; Turgut, Gurbet Celik; Sen, Alaattin; Zbancioc, Ana-Maria; Luca, Simon Vlad; Skalicka-Woźniak, Krystyna; Skiba, Adrianna; Tataringa, Gabriela (John Wiley and Sons Inc, 2022)

  Series of synthetic coumarin derivatives (1-16) were tested against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), two enzymes linked to the pathology of Alzheimer's disease (AD). Compound 16 was the most ...

• Protocol for cell surface biotinylation of magnetic labeled and captured human peripheral blood mononuclear cells 

  Ayaz-Guner, Serife; Acar, Mustafa Burak; Boyvat, Dudu; Guner, Huseyin; Bozalan, Habibe; Güzel, Melis; Yıldır, Selin Kübra; Altınsoy, Nilay; Fındık, Fatma; Karakükçü, Musa; Özcan, Servet (Cell Press, 2022)

  Analysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnetically activated cell sorting (MACS) and surface biotinylation ...

• Genomic, probiotic, and metabolic potentials of Liquorilactobacillus nagelii AGA58, a novel bacteriocinogenic motile strain isolated from lactic acid-fermented shalgam 

  Yetiman, Ahmet Evren; Ortakci, Fatih (ELSEVIER, 2023)

  This study aimed to perform genomic, probiotic, and metabolic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from a lactic acid-fermented shalgam beverage to understand its metabolic potentials and ...

• Exploring the binding capacity of lactic acid bacteria derived bacteriocins against RBD of SARS-CoV-2 Omicron variant by molecular simulations 

  Erol, Ismail; Kotil, Seyfullah Enes; Ortakci, Fatih; Durdagi, Serdar (2023)

  The changes in the SARS-CoV-2 genome have resulted in the emergence of new variants. Some of the variants have been classified as variants of concern (VOC). These strains have higher transmission rate and improved fitness. ...

• Investigation of the Interaction of Adipose-Derived Mesenchymal Stem Cells with ε-Polycaprolactone and Egg White Scaffolds 

  Oztel, Olga N.; Yilmaz, Hilal; Isoglu, Ismail Alper; Allahverdiyev, Adil (GAZİ ÜNİVERSİTESİ, 2023)

  The development of three-dimensional (3D) cell culture models is becoming increasingly important due to their numerous advantages over conventional monolayer culture. This study aimed to examine the interaction of adipose ...

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