A5037440533- Synthesis and biological activity
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Cell Image Analysis Techniques
- Image Processing Techniques and Applications
- Synthesis and Characterization of Heterocyclic Compounds
- PI3K/AKT/mTOR signaling in cancer
- AI in cancer detection
- Genomics and Phylogenetic Studies
- Cancer-related Molecular Pathways
- Cancer, Hypoxia, and Metabolism
- Gene expression and cancer classification
- Click Chemistry and Applications
- HIV/AIDS drug development and treatment
- Cancer Mechanisms and Therapy
- Biochemical and Molecular Research
- Cancer therapeutics and mechanisms
- RNA and protein synthesis mechanisms
- Quinazolinone synthesis and applications
- Synthesis and Biological Evaluation
- Genetics, Bioinformatics, and Biomedical Research
- Gene Regulatory Network Analysis
- Liver Disease Diagnosis and Treatment
- Genomics, phytochemicals, and oxidative stress
University of Chicago
2020-2025
Middle East Technical University
2015-2024
Centre for Cancer Biology
2021
Sağlık Bilimleri Üniversitesi
2019
Ankara University
2016
Bilkent University
2005-2015
Ankara (Czechia)
2015
British Institute at Ankara
2015
Atatürk University
2011
Virginia Tech
2004-2005
<h3>Importance</h3> Application of deep learning algorithms to whole-slide pathology images can potentially improve diagnostic accuracy and efficiency. <h3>Objective</h3> Assess the performance automated at detecting metastases in hematoxylin eosin–stained tissue sections lymph nodes women with breast cancer compare it pathologists' diagnoses a setting. <h3>Design, Setting, Participants</h3> Researcher challenge competition (CAMELYON16) develop solutions for node (November 2015-November...
The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of the rapamycin (mTOR) signalling pathway is hyperactivated or altered in many cancer types and regulates a broad range cellular processes including survival, proliferation, growth, metabolism, angiogenesis metastasis.
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation protein function. Results Here, we report on results third CAFA challenge, CAFA3, that featured expanded analysis over previous rounds, both in terms volume data analyzed types performed. In a novel major new development, predictions assessment goals drove some experimental assays, resulting functional annotations for...
The DEEPScreen system is composed of 704 target protein specific prediction models, each independently trained using experimental bioactivity measurements against many drug candidate small molecules, and optimized according to the binding properties proteins.
Abstract Automated protein function prediction is critical for the annotation of uncharacterized sequences, where accurate methods are still required. Recently, deep learning based have outperformed conventional algorithms in computer vision and natural language processing due to prevention overfitting efficient training. Here, we propose DEEPred, a hierarchical stack multi-task feed-forward neural networks, as solution Gene Ontology (GO) prediction. DEEPred was optimized through rigorous...
The automated prediction of the enzymatic functions uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most these studies are limited specific functional classes levels Enzyme Commission (EC) number hierarchy. Besides, previous incorporated only single input feature type, which limits applicability wide space. Here, we novel function tool, ECPred, based on ensemble machine learning classifiers.
Abstract Enhanced spatiotemporal selectivity in photonic sensitization of dissolved molecular oxygen is an important target for improving the potential and practical applications photodynamic therapy. Considering high intracellular glutathione concentrations within cancer cells, a series BODIPY‐based sensitizers that can generate cytotoxic singlet only after glutathione‐mediated cleavage electron‐sink module were designed synthesized. Cell culture studies not validate our design, but also...
The relative ranking of cirrhosis-related deaths differs between high-/middle-income countries. Gut microbiome is affected in cirrhosis and related to diet. Our aim was determine the effect differing dietary habits on gut microbiota clinical outcomes. Outpatient compensated/decompensated patients with controls from Turkey United States underwent stool analysis. Patients were followed till 90-day hospitalizations. Shannon diversity multivariable determinants (Cox binary logistic) microbial...
Activation of the PI3K/Akt/mTOR pathway is an important signaling mechanism involved in development and progression liver cancer stem cell (LCSC) population during acquired Sorafenib resistance advanced hepatocellular carcinoma (HCC). Therefore, identification novel therapeutic targets involving this acting on LCSCs highly essential. Here, we analyzed bioactivities molecular pathways action small-molecule inhibitors comparison with Sorafenib, DNA intercalators, DAPT (CSC inhibitor)...
Abstract Motivation Identification of interactions between bioactive small molecules and target proteins is crucial for novel drug discovery, repurposing uncovering off-target effects. Due to the tremendous size chemical space, experimental bioactivity screening efforts require aid computational approaches. Although deep learning models have been successful in predicting compounds, effective comprehensive featurization proteins, be given as input neural networks, remains a challenge. Results...
Abstract Despite decades of intensive search for compounds that modulate the activity particular protein targets, a large proportion human kinome remains as yet undrugged. Effective approaches are therefore required to map massive space unexplored compound–kinase interactions novel and potent activities. Here, we carry out crowdsourced benchmarking predictive algorithms kinase inhibitor potencies across multiple families tested on unpublished bioactivity data. We find top-performing...
Utilizing AI-driven approaches for drug-target interaction (DTI) prediction require large volumes of training data which are not available the majority target proteins. In this study, we investigate use deep transfer learning interactions between drug candidate compounds and understudied proteins with scarce data. The idea here is to first train a neural network classifier generalized source dataset size then reuse pre-trained as an initial configuration re-training/fine-tuning purposes...
Abstract Motivation: Availability of the sequences entire genomes shifts scientific curiosity towards identification function in large scale as genome studies. In near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate a result proteomics this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing effectively. Results: We define ontology comprehensive representation events. The presented here...
Idiopathic pulmonary fibrosis is a fatal interstitial lung disease characterized by the TGF-β (transforming growth factor-β)–dependent differentiation of fibroblasts into myofibroblasts, which leads to excessive deposition collagen proteins and progressive scarring. We have previously shown that synthesis myofibroblasts requires de novo glycine, most abundant amino acid found in protein. upregulates expression enzymes serine–glycine pathway fibroblasts; however, transcriptional signaling...
More rapid and accurate high-throughput screening in molecular cellular biology research has become possible with the development of automated microscopy imaging, for which cell nucleus segmentation commonly constitutes core step. Although several promising methods exist segmenting nuclei monolayer isolated less-confluent cells, it still remains an open problem to segment more-confluent tend grow overlayers. To address this problem, we propose a new model-based algorithm. This algorithm...
Senescence is a permanent proliferation arrest in response to cell stress such as DNA damage. It contributes strongly tissue aging and serves major barrier against tumor development. Most cells are believed bypass the senescence (become "immortal") by inactivating growth control genes TP53 CDKN2A. They also reactivate telomerase reverse transcriptase. Senescence-to-immortality transition accompanied phenotypic biochemical changes mediated genome-wide transcriptional modifications. This...
// Carolina Simioni 1 , Alberto M. Martelli 2,3,4 Alice Cani Rengul Cetin-Atalay 5 James A. McCubrey 6 Silvano Capitani Luca Neri Department of Morphology, Surgery and Experimental Medicine, University Ferrara, Italy, 2 Biomedical Neuromotor Sciences, Bologna, Italy; 3 Institute Molecular Genetics, National Research Council, Pavia, 4 Muscoloskeletal Cell Biology Laboratory, IOR, Italy Bilkent University, Ankara, Turkey Microbiology & Immunology, Brody School East Greenville, NC, USA....
Particulate matter (PM) air pollution causes cardiopulmonary mortality via macrophage-driven lung inflammation; however, the mechanisms are incompletely understood. RNA-sequencing demonstrated Acod1 (Aconitate decarboxylase 1) as one of top genes induced by PM in macrophages. encodes a mitochondrial enzyme that produces itaconate, which has been shown to exert anti-inflammatory effects NRF2 after LPS. Here, we demonstrate induces and reduced respiration complex II inhibition. Using Acod1-/-...
Cellular metabolism is a critical regulator of macrophage effector function. Tissue-resident alveolar macrophages (TR-AMs) inhabit unique niche marked by high oxygen and low glucose. We have recently shown that in contrast to bone marrow-derived (BMDMs), TR-AMs do not utilize glycolysis instead predominantly rely on mitochondrial function for their response. It known how changes local concentration occur during conditions such as acute respiratory distress syndrome (ARDS) might affect TR-AM...
Idiopathic pulmonary fibrosis is a fatal disease characterized by the TGF-β-dependent activation of lung fibroblasts, leading to excessive deposition collagen proteins and progressive replacement healthy with scar tissue. We others have shown that TGF-β-mediated Mechanistic Target Rapamycin Complex 1 (mTORC1) downstream upregulation Activating Transcription Factor 4 (ATF4) promote metabolic reprogramming in fibroblasts de