Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Author: search.filters.author.Gönen, MehmetScopus Q: search.filters.scopusQuartile.Q1

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  • Article
    Citation - WoS: 560
    Citation - Scopus: 607
    A Community Effort To Assess and Improve Drug Sensitivity Prediction Algorithms
    (Nature Publishing Group, 2014) Costello, James C.; Heiser, Laura M.; Georgii, Elisabeth; Gönen, Mehmet; Menden, Michael P.; Wang, Nicholas J.; Bansal, Mukesh; Ammad-ud-din, Muhammad; Hintsanen, Petteri; Khan, Suleiman A.; Mpindi, John-Patrick; Kallioniemi, Olli; Honkela, Antti; Aittokallio, Tero; Wennerberg, Krister; NCI-DREAM Community; Karaçalı, Bilge; Collins, James J.; Gallahan, Dan; Singer, Dinah; Saez-Rodriguez, Julio; Kaski, Samuel; Gray, Joe W.; Stolovitzky, Gustavo
    Predicting the best treatment strategy from genomic information is a core goal of precision medicine. Here we focus on predicting drug response based on a cohort of genomic, epigenomic and proteomic profiling data sets measured in human breast cancer cell lines. Through a collaborative effort between the National Cancer Institute (NCI) and the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we analyzed a total of 44 drug sensitivity prediction algorithms. The top-performing approaches modeled nonlinear relationships and incorporated biological pathway information. We found that gene expression microarrays consistently provided the best predictive power of the individual profiling data sets; however, performance was increased by including multiple, independent data sets. We discuss the innovations underlying the top-performing methodology, Bayesian multitask MKL, and we provide detailed descriptions of all methods. This study establishes benchmarks for drug sensitivity prediction and identifies approaches that can be leveraged for the development of new methods.
  • Article
    Citation - WoS: 60
    Citation - Scopus: 66
    Preparation and Characterization of Calcium Stearate Powders and Films Prepared by Precipitation and Langmuir-Blodgett Techniques
    (American Chemical Society, 2010) Gönen, Mehmet; Öztürk, Serdar; Balköse, Devrim; Okur, Salih; Ülkü, Semra
    The preparation of calcium stearate (CaSt2) using precipitation and Langmuir-Blodgett techniques was investigated in this study. While sodium stearate and calcium chloride were used in the precipitation process, calcium stearate nanofilms were produced from stearic acid and calcium chloride in sodium borate buffer with the Langmuir-Blodgett technique. Fourier transform infrared (FTIR) spectroscopy indicated carboxylate bands at 1577 and 1543 cm-1 in equal intensity in the powder form, but the films had a higher intensity 1577 cm-1 band than the 1543 cm-1 band. This showed the calcium ions associated with the COO- ions in the monodendate and bidendate structures in powders, and it was mainly in the bidendate structure in films. While characteristic peaks of CaSt2 at 2θ values of 6.40° and 19.58° were obtained in the X-ray diffraction (XRD) pattern of the dried powdered product, no sharp peaks were present in the 13 layer CaSt2 film. From scanning electron microscopy (SEM) micrographs, it was seen that calcium stearate powder had lamellar structure and the average particle size was 600 nm. The AFM picture of the CaSt2 film indicated the surface was not smooth with a peak to valley distance of 6 nm. © 2010 American Chemical Society.
  • Article
    Citation - WoS: 22
    Citation - Scopus: 28
    The Effect of Zinc Stearate on Thermal Degradation of Paraffin Wax
    (Springer Verlag, 2008) Gönen, Mehmet; Balköse, Devrim; İnal, Fikret; Ülkü, Semra
    In this research, the effects of zinc stearate addition on paraffin wax degradation were investigated by differential scanning calorimetry (DSC) and thermogravimetry (TG). The apparent activation energies of wax decomposition in nitrogen and air atmospheres were determined as 76 and 37 kJ mol-1, respectively applying Kissinger method to TG data. The degradation rate constants of paraffin containing zinc stearate (0.1-0.5%) were found to be almost two times greater than that of paraffin only in air atmosphere. However, zinc stearate did not affect the rate constants in nitrogen significantly.