• Determining the C-terminal amino acid of a peptide from MS/MS data 

  Allmer, Jens (Proteomass Scientific Society, 2013-12)

  Proteomics is currently chiefly based on mass spectrometry (MS) which is the tool of choice to investigate proteins. Two computational approaches to derive the tandem mass spectrum precursor’s sequence are widely employed. ...

• Nanocarriers for plant-derived natural compounds 

  Bayraktar, Oğuz; Erdoğan, İpek; Köse, Merve D.; Kalmaz, Gülcan (Elsevier, 2017-05)

  Natural products constitute a large fraction in drug discovery processes. The term includes compounds from plants, microorganisms, and animals. Most of the natural products are secondary metabolites derived from plants, ...

• Small RNA data set that includes tRNA-derived fragments from Jurkat cells treated with camptothecin 

  Coşacak, Mehmet İlyas; Erdoğan, İpek; Nalbant, Ayten; Akgül, Bünyamin (Elsevier, 2018-04)

  In this article, we report a small RNA data set obtained from human T cell acute leukemia Jurkat cells, which were treated with the universal apoptotic agent camptothecin. Based on the Annexin-V labeling pattern, we sorted ...

• Re-arrangements in the cytoplasmic distribution of small RNAs following the maternal-to-zygotic transition in Drosophila embryos 

  Coşacak, Mehmet İlyas; Yiğit, Hatice; Kızıl, Çağhan; Akgül, Bünyamin (MDPI, 2018-02)

  Small ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate ...

• The expressed MicroRNA-mRNA interactions of Toxoplasma gondii 

  Acar, İlhan Erkin; Saçar Demirci, Müşerref Duygu; Groß, Uwe; Allmer, Jens (Frontiers Media S.A., 2018-01)

  MicroRNAs (miRNAs) are involved in post-transcriptional modulation of gene expression and thereby have a large influence on the resulting phenotype. We have previously shown that miRNAs may be involved in the communication ...

• Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis 

  Erdoğan, İpek; Coşacak, Mehmet İlyas; Nalbant, Ayten; Akgül, Bünyamin (TUBITAK, 2018)

  MicroRNAs (miRNAs) are small noncoding RNAs of about 19-25 nt that regulate gene expression posttranscriptionally under various cellular conditions, including apoptosis. The miRNAs involved in modulation of apoptotic events ...

• The importance of boron in biological systems 

  Uluışık, İrem; Karakaya, Hüseyin Çağlar; Koç, Ahmet (Elsevier, 2018-01)

  Boron is an essential element for plants and probably essential for human and animal health. Boron has a broad range of physiological effects on biological systems at low concentrations, whereas it is toxic to at high ...

• Biofabrication of in situ self assembled 3D cell cultures in a weightlessness environment generated using magnetic levitation 

  Anıl İnevi, Müge; Yaman, Sena; Arslan Yıldız, Ahu; Meşe, Gülistan; Yalçın Özuysal, Özden; Tekin, Hüseyin Cumhur; Özçivici, Engin (Nature Publishing, 2018-12)

  Magnetic levitation though negative magnetophoresis is a novel technology to simulate weightlessness and has recently found applications in material and biological sciences. Yet little is known about the ability of the ...

• Cell proliferation and cytotoxicity assays 

  Adan, Aysun; Kiraz, Yağmur; Baran, Yusuf (Bentham Science, 2016-11)

  Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival ...

• The second case of saposin a deficiency and altered autophagy 

  Köse, Melis; Akyıldız Demir, Seçil; Akıncı, Gülçin; Eraslan, Cenk; Yılmaz, Ünsal; Ceylaner, Serdar; Sözmen Yıldırım, Eser; Seyrantepe, Volkan (Springer, 2018)

  Krabbe disease is a lysosomal storage disease caused by galactosylceramidase deficiency, resulting in neurodegeneration with a rapid clinical downhill course within the first months of life in the classic infantile ...

• Determination of the effects of biomaterials on human peripheral blood mononuclear cells (PBMC) 

  Sudağıdan, Mert; Güneş, Hatice; Harsa, Şebnem (European IOS Press, 2002)

• Cellular distribution of invadopodia is regulated by nanometer scale surface protein patterns 

  Batı Ayaz, Gizem; Can, Ali; Pesen Okvur, Devrim (Elsevier, 2017-10)

  Invadopodia are proteolytic structures formed by cancer cells. It is not known whether their cellular distribution can be regulated by the organization of the extracellular matrix or the organization of the golgi complex ...

• Environmentally responsive dual-targeting nanoparticles: Improving drug accumulation in cancer cells as a way of preventing anticancer drug efflux 

  Dağlıoğlu, Cenk (American Pharmacists Association, 2018-03)

  Drug targeting and stimuli-responsive drug release are 2 active areas of cancer research and hold tremendous potential in the management of cancer drug resistance. In this study, I addressed this issue and focused on the ...

• Plant-microbe interactions in phytoremediation 

  Özyiğit, İbrahim İlker; Doğan, İlhan (Elsevier, 2014)

  Our atmosphere, water resources and soil are becoming increasingly contaminated with inorganic and organic compounds as a result of anthropogenic-driven inputs, mainly from industry, mining, motorized traffic, agriculture, ...

• Intersection of MicroRNA and gene regulatory networks and their implication in cancer 

  Yousef, Malik; Trinh, Hung V.; Allmer, Jens (Bentham Science Publishers, 2014-09)

  MicroRNAs (miRNAs) have attracted heightened attention for their role as post-transcriptional regulators of gene expression. It has become clear that miRNAs can both up- and downregulate protein expression. According to ...

• Computational and bioinformatics methods for microRNA gene prediction 

  Allmer, Jens (Springer, 2014)

  MicroRNAs (miRNAs) have attracted ever-increasing interest in recent years. Since experimental approaches for determining miRNAs are nontrivial in their application, computational methods for the prediction of miRNAs have ...

• Computational methods for microRNA target prediction 

  Hamzeiy, Hamid; Yousef, Malik; Allmer, Jens (Springer, 2014)

  MicroRNAs (miRNAs) are important players in gene regulation. The final and maybe the most important step in their regulatory pathway is the targeting. Targeting is the binding of the miRNA to the mature RNA via the RNA-induced ...

• Physiology of metabolites 

  Frary, Amy; Frary, Anne (CABI Publishing, 2012-02)

  This chapter provides an overview of recent research on the effects of genotype fruit development and growing conditions on the synthesis and concentrations of the following metabolites in pepper (Capsicum spp.): antioxidants, ...

• Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers 

  Yousef, Malik; Nigatu, Dawit; Levy, Dalit; Allmer, Jens; Henkel, Werner (Springer, 2017-12)

  Background: Diseases like cancer can manifest themselves through changes in protein abundance, and microRNAs (miRNAs) play a key role in the modulation of protein quantity. MicroRNAs are used throughout all kingdoms and ...

• Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action 

  Neergheen-Bhujun, Vidushi; Awan, Almas Taj; Baran, Yusuf; Bunnefeld, Nils; Chan, Kit; Dela Cruz, Thomas Edison; Egamberdieva, Dilfuza; Elsasser, Simon; Johnson, Mari-Vaughn V.; Komai, Shoji; Konevega, Andrey L.; Malone, John H.; Mason, Paul; Nguon, Rothsophal; Piper, Ross; Shrestha, Uttam Babu; Pesic, Milica; Kagansky, Alexander (University of Edinburgh, 2017-11)

  Looking to nature for medicine is nothing new – we have been doing it for tens of thousands of years and although modern pharmaceutical science has come a long way from those ancient roots, nature is and will always be ...

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