• 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 ...

• 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 ...

• 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 ...

• 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, ...

• 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 ...

• miRcorrNetPro: Unraveling Algorithmic Insights through Cross-Validation in Multi-Omics Integration for Comprehensive Data Analysis 

  Yazici, Miray Unlu; Yousef, Malik; Marron J.S.; Bakir-Gungor, Burcu (Institute of Electrical and Electronics Engineers Inc., 2023)

  High throughput -omics technologies facilitate the investigation of regulatory mechanisms of complex diseases. Along this line, scientists develop promising tools and methods to extend our understanding at the molecular ...

• Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics 

  Gumustop, Ismail; Ortakci, Fatih (Frontiers Media S.A., 2023)

  Leuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides ...

• Can mesenchymal stem/stromal cells and their secretomes combat bacterial persisters? 

  Bicer-Çalışkan, Mesude; Fidan, Ozkan (SPRINGER, 2023)

  The increasing number of life-threatening infections caused by persister bacteria is associated with various issues, including antimicrobial resistance and biofilm formation. Infections due to persister cells are often ...

• Exploring therapeutic avenues: mesenchymal stem/stromal cells and exosomes in confronting enigmatic biofilm-producing fungi 

  Bicer, Mesude (SPRINGER, 2024)

  Fungal infections concomitant with bioflms can demonstrate an elevated capacity to withstand substantially higher concentrations of antifungal agents, contrasted with infectious diseases caused by planktonic cells. This ...

• Alantolactone ameliorates graft versus host disease in mice 

  Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Şerife; Çakır, Mustafa; Özcan, Alper; Yılmaz, Ebru; Karakukcu, Musa; Donmez-Altuntas, Hamiyet; Yay, Arzu Hanim; Deniz, Kemal; Altay, Derya; Arslan, Duran; Canatan, Halit; Eken, Ahmet; Unal, Ekrem (ELSEVIER, 2024)

  The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate ...

• HER2-Specific Peptide (LTVSPWY) and Antibody (Herceptin) Targeted Core Cross-Linked Micelles for Breast Cancer: A Comparative Study 

  Bayram, Nazende Nur; Ulu, Gizem Tuğçe; Abdulhadi, Nusaibah Abdulsalam; Gürdap, Seda; İşoğlu, İsmail Alper; Baran, Yusuf; İşoğlu, Sevil Dinçer (MDPI, 2023)

  This study aims to prepare a novel breast cancer-targeted micelle-based nanocarrier, which is stable in circulation, allowing intracellular drug release, and to investigate its cytotoxicity, apoptosis, and cytostatic ...

• Comparative genomics of Loigolactobacillus coryniformis with an emphasis on L. coryniformis strain FOL-19 isolated from cheese 

  Gumustop, Ismail; Ortakci, Fatih (ELSEVIER, 2023)

  Loigolactobacillus coryniformis is a member of lactic acid bacteria isolated from various ecological niches. We isolated a novel L. coryniformis strain FOL-19 from artisanal Tulum cheese and performed the whole-genome ...

• Histopathology image classification: highlighting the gap between manual analysis and AI automation 

  Doğan, Refika Sultan; Yılmaz, Bülent (FRONTIERS MEDIA SA, 2023)

  The field of histopathological image analysis has evolved significantly with the advent of digital pathology, leading to the development of automated models capable of classifying tissues and structures within diverse ...

• A comprehensive study on automatic non-informative frame detection in colonoscopy videos 

  Kaçmaz, Rukiye Nur; Doğan, Refika Sultan; Yılmaz, Bülent (WILEY, 2024)

  Despite today's developing healthcare technology, conventional colonoscopy is still a gold-standard method to detect colon abnormalities. Due to the folded structure of the intestine and visual disturbances caused by ...

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