A5043036637- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Mass Spectrometry Techniques and Applications
- RNA Interference and Gene Delivery
- Metabolomics and Mass Spectrometry Studies
- RNA Research and Splicing
- Circular RNAs in diseases
- Gene expression and cancer classification
- Toxoplasma gondii Research Studies
- Identification and Quantification in Food
- Research Data Management Practices
- Scientific Computing and Data Management
- Smart Agriculture and AI
- Bioinformatics and Genomic Networks
- Chromosomal and Genetic Variations
- Genetics, Bioinformatics, and Biomedical Research
- Aluminum toxicity and tolerance in plants and animals
- Genetic and Environmental Crop Studies
- Plant Stress Responses and Tolerance
- Glycosylation and Glycoproteins Research
Ruhr West University of Applied Sciences
2019-2024
Izmir Institute of Technology
2010-2021
Wageningen University & Research
2018-2021
Institute of Bioinformatics and Applied Biotechnology
2019
İzmir University of Economics
2007-2008
University of Münster
2006-2007
University of Pennsylvania
2006-2007
Joint Genome Institute
2007
Institut de Biologie Physico-Chimique
2007
Sorbonne Université
2007
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It model system for studying chloroplast-based photosynthesis, as well the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited common ancestor animals, but lost in plants. We sequenced ∼120-megabase nuclear genome performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated...
The basic question addressed in this study is how energy metabolism adjusted to cope with iron deficiency Chlamydomonas reinhardtii. To investigate the impact of on bioenergetic pathways, comparative proteomics was combined spectroscopic as well voltametric oxygen measurements assess protein dynamics linked functional properties respiratory and photosynthetic machineries. Although electron transfer largely compromised under deficiency, our quantitative data revealed that antenna size...
Abstract Background Cell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, or their products do not act alone but within networks. Subsets these networks be viewed as modules that provide specific functionality an organism. The Kyoto encyclopedia genomes (KEGG) systematically analyzes gene functions, proteins, molecules combines them into pathways. Measurements expression (e.g., RNA-seq data) mapped KEGG pathways determine...
Lithium is a mood stabilizing agent commonly used for the treatment of bipolar disorder. Here, we investigated potential neuroprotective effect lithium against paraquat toxicity and its underlying mechanisms in vitro. SH-SY5Y human neuroblastoma cells were treated with (PQ) 0.5 mM concentration after pretreatment to test lithium's capability preventing cell toxicity. Cell death was evaluated by LDH, WST-8, tryphan blue assays. Apoptosis analyzed using DNA fragmentation, Annexin V...
Abstract The treatment of human diseases is a major research question in many fields related to medicine. It has become clear that patient stratification utmost importance so patients receive the best possible treatment. Bio/disease markers are critical achieve stratification. Markers can come from different sources such as genomics, transcriptomics, and proteomics. Establishing measurements often involves data analysis, machine learning, feature selection. Traditional selection techniques...
MicroRNAs (miRNAs), a class of small, non-coding RNAs, play pivotal role in regulating gene expression at the post-transcriptional level. These regulatory molecules are integral to many biological processes and have been implicated pathogenesis various diseases, including Human Immunodeficiency Virus (HIV) infection. This review aims cover current understanding multifaceted roles miRNAs assume context HIV infection pathogenesis. The discourse is structured around three primary focal points:...
MicroRNAs are crucial for post-transcriptional gene regulation, and their dysregulation has been associated with diseases like cancer and, therefore, analysis become popular. The experimental discovery of miRNAs is cumbersome thus, many computational tools have proposed. Here we assess 13 ab initio pre-miRNA detection approaches using all relevant, published, novel data sets while judging algorithm performance based on ten intrinsic measures. We present an extensible framework, izMiR, which...
Erythropoietin (EPO) is a neuroprotective cytokine, which has been applied in several animal models presenting neurological disorders. One of the proposed modes action resulting neuroprotection post-transcriptional gene expression regulation. This directly brings to mind microRNAs (miRNAs), are small non-coding RNAs that regulate at level. It not yet evaluated whether miRNAs participate biological effects EPO or it, inversely, modulates specific neuronal cells. In this study, we employed...
Abstract Motivation Disease is often manifested via changes in transcript and protein abundance. MicroRNAs (miRNAs) are instrumental regulating abundance may measurably influence levels. miRNAs target more than one mRNA (for humans, the average three), mRNAs targeted by miRNA genes considered this study, also three). Therefore, it difficult to determine that cause observed differential gene expression. We present a novel approach, maTE, which based on machine learning, integrates information...
A new high-throughput computational strategy was established that improves genomic data mining from MS experiments. The MS/MS were analyzed by the SEQUEST search algorithm and a combination of de novo amino acid sequencing in conjunction with an error-tolerant database tool, operating on 256 processor computer cluster. previously as GenomicPeptideFinder (GPF), enables detection intron-split and/or alternatively spliced peptides when deduced DNA. Isolated thylakoid membranes eukaryotic green...
MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post-transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the microprocessor complex, yielding a hairpin structure. Which then exported into cytosol where it processed Dicer incorporated RNA-induced silencing complex. All these biogenesis steps add overall specificity miRNA production effect. Unfortunately, their...
Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is an orphan crop species with most molecular genetic research work done in the last decade. In this study, we used a pyrosequencing approach for development of genomic simple-sequence repeat (SSR) markers sesame. Our proved successful identifying 19,816 nonredundant SSRs, 5727 which were identified contig assembly that covers 19.29% sesame genome. Mononucleotide repeats abundant SSR type genome (48.5% all SSRs), followed by dinucleotide...
Abstract MicroRNAs (miRNAs) were discovered two decades ago, yet there is still a great need for further studies elucidating their genesis and targeting in different phyla. Since experimental discovery validation of miRNAs difficult, computational predictions are indispensable today most approaches employ machine learning. Toxoplasma gondii, parasite residing within the cells its hosts like human, uses post-transcriptional gene regulation. It may also regulate hosts’ expression, which has...
MicroRNAs (miRNAs) are short RNA sequences that guide post-transcriptional regulation of gene expression via complementarity to their target mRNAs. Discovered only recently, miRNAs have drawn a lot attention. Multiple protein complexes interact first cleave hairpin from nascent RNA, export it into the cytosol, trim its loop, and incorporate RISC complex which is important for binding mRNA. This process works within one cell, but circulating been described suggesting role in cell-cell...
Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play key role in the modulation translation efficiency. Known pre-miRNAs are listed miRBase, they have been discovered variety organisms ranging from viruses microbes to eukaryotic organisms. The computational detection is great interest, such approaches usually employ machine learning discriminate between miRNAs other sequences. Many features proposed describing pre-miRNAs, we previously...
Experimental detection and validation of miRNAs is a tedious, time-consuming, expensive process. Computational methods for miRNA gene are being developed so that the number candidates need experimental can be reduced to manageable amount. involve homology-based ab inito algorithms. Both approaches dependent on positive negative training examples. Positive examples usually derived from miRBase, main resource experimentally validated miRNAs. We encountered some problems with miRBase which we...
MicroRNAs (miRNAs) are short RNA sequences involved in posttranscriptional gene regulation. Their experimental analysis is complicated and, therefore, needs to be supplemented with computational miRNA detection. Currently detection mainly performed using machine learning and particular two-class classification. For learning, the miRNAs need parametrized more than 700 features have been described. Positive training examples for readily available, but negative data hard come by. Therefore, it...