Now showing items 1-20 of 41

    • Assessment and correction of errors in DNA sequencing technologies 

      Fırtına, Can (Bilkent University, 2018-01)
      Next Generation Sequencing technologies differ by several parameters where the choice to use whether short or long read sequencing platforms often leads to trade-offs between accuracy and read length. In this thesis, I ...
    • Biological properties of extracellular vesicles and their physiological functions 

      Yáñez-Mó, M.; Siljander, P. R. M.; Andreu, Z.; Zavec, A. B.; Borràs, F. E.; Buzas, E. I.; Buzas, K.; Casal, E.; Cappello, F.; Carvalho, J.; Colás, E.; Cordeiro-Da, S. A.; Fais, S.; Falcon-Perez, J. M.; Ghobrial, I. M.; Giebel, B.; Gimona, M.; Graner, M.; Gursel, I.; Gursel, M.; Heegaard, N. H. H.; Hendrix, A.; Kierulf, P.; Kokubun, K.; Kosanovic, M.; Kralj-Iglic, V.; Krämer-Albers, E. M.; Laitinen, S.; Lässer, C.; Lener, T.; Ligeti, E.; Line, A.; Lipps, G.; Llorente, A.; Lötvall, J.; Manček-Keber, M.; Marcilla, A.; Mittelbrunn, M.; Nazarenko, I.; Nolte-'t Hoen, E. N. M.; Nyman, T. A.; O'Driscoll, L.; Olivan, M.; Oliveira, C.; Pállinger, E.; Del Portillo, H. A.; Reventós, J.; Rigau, M.; Rohde, E.; Sammar, M.; Sánchez-Madrid, F.; Santarém, N.; Schallmoser, K.; Ostenfeld, M. S.; Stoorvogel, W.; Stukelj, R.; Grein V. D. S.G.; Helena,ü V. M.; Wauben, M. H. M.; De Wever, O. (Taylor & Francis, 2015)
      In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and ...
    • Building and improving reference genome assemblies: this paper reviews the problems and algorithms of assembling a complete genome from millions of short DNA sequencing reads 

      Steinberg, K. M.; Schneider, V. A.; Alkan C.; Montague, M. J.; Warren, W. C.; Church, D. M.; Wilson, R. K. (Institute of Electrical and Electronics Engineers Inc., 2017)
      A genome sequence assembly provides the foundation for studies of genotypic and phenotypic variation, genome structure, and evolution of the target organism. In the past four decades, there has been a surge of new sequencing ...
    • Chromatin-modifying enzymes as modulators of reprogramming 

      Onder, T. T.; Kara, N.; Cherry, A.; Sinha, A. U.; Zhu, N.; Bernt, K. M.; Cahan, P.; Marcarci, B. O.; Unternaehrer, J.; Gupta, P. B.; Lander, E. S.; Armstrong, S. A.; Daley, G. Q. (Nature Publishing Group, 2012)
      Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic ...
    • A chronic myeloid leukemia-like syndrome case with del (12) (p12) in a Li-Fraumeni syndrome family 

      Guran, Ş.; Beyan, C.; Nevruz, O.; Yakıcıer, C.; Tunca, Y. (Blackwell Publishing Ltd, 2005)
      Li-Fraumeni syndrome is a familial cancer syndrome characterized by different tumors and hereditary p53 mutations. Here, a chronic myeloid leukemia-like syndrome case in a Li-Fraumeni syndrome family with del (12) (p12) ...
    • Comment on "modeling the electrical conduction in DNA nanowires: Charge transfer and lattice fluctuation theories" 

      Panahi M.; Chitsazanmoghaddam M. (American Physical Society, 2016)
      In a recent paper [S. Behnia and S. Fathizadeh, Phys. Rev. E 91, 022719 (2015)10.1103/PhysRevE.91.022719] an analytical approach is proposed for the investigation of the conductivity properties of DNA. The authors use mean ...
    • Comparison of Au(III) and Ga(III) ions' binding to calf thymus DNA: Spectroscopic characterization and thermal analysis 

      Sarioglu O.F.; Tekiner-Gursacli, R.; Ozdemir, A.; Tekinay, T. (Humana Press Inc.Springer, 2014)
      Metals have been studied as potential chemotherapeutic agents for cancer therapies due to their high reactivity toward a wide variety of substances. The characterization of metal ion-binding capacities is essential to ...
    • Correlation-induced DNA adsorption on like-charged membranes 

      Buyukdagli S.; Blossey R. (American Physical Society, 2016)
      The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains ...
    • Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair 

      Dal, G. M.; Ergüner, B.; Saǧıroǧlu, M. S.; Yüksel, B.; Onat, O. E.; Alkan C.; Özçelik, T. (B M J Group, 2014)
      Background: Human de novo single-nucleotide variation (SNV) rate is estimated to range between 0.82-1.70×10-8 mutations per base per generation. However, contribution of early postzygotic mutations to the overall human de ...
    • Electrostatic energy barriers from dielectric membranes upon approach of translocating DNA molecules 

      Buyukdagli S.; Ala-Nissila T. (A I P Publishing LLC, 2016)
      We probe the electrostatic cost associated with the approach phase of DNA translocation events. Within an analytical theory at the Debye-Hückel level, we calculate the electrostatic energy of a rigid DNA molecule interacting ...
    • Electrostatics of Polymer Translocation Events in Electrolyte Solutions 

      Buyukdagli, S.; Ala-Nissila, T. (American Institute of Physics Inc., 2016)
      We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral ...
    • Enhanced immunostimulatory activity of cyclic dinucleotides on mouse cells when complexed with a cell-penetrating peptide or combined with CpG 

      Yildiz, S.; Alpdundar, E.; Gungor, B.; Kahraman, T.; Bayyurt, B.; Gursel, I.; Gursel, M. (Wiley - V C H Verlag GmbH & Co. KGaA, 2015)
      Recognition of pathogen-derived nucleic acids by immune cells is critical for the activation of protective innate immune responses. Bacterial cyclic dinucleotides (CDNs) are small nucleic acids that are directly recognized ...
    • Extremely skewed X-chromosome inactivation patterns in women with recurrent spontaneous abortion 

      Bagislar, S.; Ustuner, I.; Cengiz, B.; Soylemez, F.; Akyerli, C. B.; Ceylaner, S.; Ceylaner, G.; Acar, A.; Ozcelik, T. (Wiley-Blackwell Publishing Asia, 2006)
      Background: The role of extremely skewed X-chromosome inactivation (XCI) has been questioned in the pathogenesis of recurrent spontaneous abortion (RSA) but the results obtained were conflicting. Aims: We therefore ...
    • Fast and accurate mapping of complete genomics reads 

      Lee, D.; Hormozdiari, F.; Xin, H.; Hach, F.; Mutlu, O.; Alkan C. (Academic Press, 2015)
      Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of ...
    • Functional genomics in translational cancer research: focus on breast cancer 

      Yulug, I. G.; Gur-Dedeoglu, B. (Oxford University Press, 2008)
      Conventional molecular and genetic methods for studying cancer are limited to the analysis of one locus at a time. A cluster of genes that are regulated together can be identified by DNA microarray, and the functional ...
    • Generation of phospholipid vesicle-nanotube networks and transport of molecules therein 

      Jesorka, A.; Stepanyants, N.; Zhang H.; Ortmen, B.; Hakonen, B.; Orwar O. (2011)
      We describe micromanipulation and microinjection procedures for the fabrication of soft-matter networks consisting of lipid bilayer nanotubes and surface-immobilized vesicles. These biomimetic membrane systems feature ...
    • Genome sequencing highlights the dynamic early history of dogs 

      Freedman, A. H.; Gronau I.; Schweizer, R. M.; Ortega-Del Vecchyo, D.; Han, E.; Silva, P. M.; Galaverni, M.; Fan, Z.; Marx P.; Lorente-Galdos, B.; Beale, H.; Ramirez, O.; Hormozdiari, F.; Alkan C.; Vilà, C.; Squire K.; Geffen, E.; Kusak, J.; Boyko, A. R.; Parker, H. G.; Lee C.; Tadigotla, V.; Siepel, A.; Bustamante, C. D.; Harkins, T. T.; Nelson, S. F.; Ostrander, E. A.; Marques Bonet, T.; Wayne, R. K.; Novembre, J. (Public Library of Science, 2014)
      To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of ...
    • Germline hMSH2 and hMLH1 gene mutations in incomplete HNPCC families 

      Wang, Q.; Desseigne, F.; Lasset, C.; Saurin J. C.; Navarro, C.; Yagci, T.; Keser I.; Bagci, H.; Luleci, G.; Gelen, T.; Chayvialle, J.-A.; Puisieux, A.; Ozturk, M. (1997)
      Hereditary non-polyposis colon cancer (HNPCC) is a common hereditary disease characterized by a predisposition to an early onset of colorectal cancer. The majority of the HNPCC families carry germline mutations of either ...
    • A high-coverage genome sequence from an archaic Denisovan individual 

      Meyer, M.; Kircher, M.; Gansauge, Marie-Theres; Li, H.; Racimo, F.; Mallick, S.; Schraiber, J. G.; Jay, F.; Prüfer, K.; Filippo, Cesare de; Sudmant, P. H.; Alkan C.; Fu, Q.; Do, R.; Rohland, N.; Tandon, A.; Siebauer, M.; Green, R. E.; Bryc, K.; Briggs, A. W.; Stenzel, U.; Dabney, J.; Shendure, J.; Kitzman, J.; Hammer, M. F.; Shunkov, M. V.; Derevianko, A. P.; Patterson, N.; Andrés, A. M.; Eichler, E. E.; Slatkin, M.; Reich, D.; Kelso, J.; Pääbo, S. (American Association for the Advancement of Science (A A A S), 2012-10-12)
      We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30x) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation ...
    • Human MLH1 deficiency predisposes to hematological malignancy and neurofibromatosis type 1 

      Ricciardone, M. D.; Özçelik, T.; Cevher, B.; Özdaǧ, H.; Tuncer, M.; Gürgey, A.; Uzunalimoǧlu, O.; Çetinkaya, H.; Tanyeli, A.; Erken, E.; Öztürk, M. (American Association for Cancer Research, 1999)
      Heterozygous germ-line mutations in the DNA mismatch repair genes lead to hereditary nonpolyposis colorectal cancer. The disease susceptibility of individuals who constitutionally lack both wild-type alleles is unknown. ...