Now showing items 1-18 of 18

    • Algorithms for effective querying of compound graph-based pathway databases 

      Dogrusoz, U.; Cetintas, A.; Demir, E.; Babur, O. (BioMed Central Ltd., 2009)
      Background: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate ...
    • 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 ...
    • ChiBE: interactive visualization and manipulation of BioPAX pathway models 

      Babur, O.; Dogrusoz, U.; Demir, E.; Sander, C. (Oxford University Press, 2010)
      SUMMARY: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large ...
    • Digital holographic microscopy of phase separation in multicomponent lipid membranes 

      Rad V.F.; Moradi A.-R.; Darudi A.; Tayebi L. (SPIE, 2016)
      Lateral in-homogeneities in lipid compositions cause microdomains formation and change in the physical properties of biological membranes. With the presence of cholesterol and mixed species of lipids, phospholipid membranes ...
    • Engineering sensorial delay to control phototaxis and emergent collective behaviors 

      Mijalkov, M.; McDaniel, A.; Wehr, J.; Volpe, G. (American Physical Society, 2016-01)
      Collective motions emerging from the interaction of autonomous mobile individuals play a key role in many phenomena, from the growth of bacterial colonies to the coordination of robotic swarms. For these collective behaviors ...
    • Genetic education and the challenge of genomic medicine development of core competences to support preparation of health professionals in Europe 

      Skirton, H.; Lewis, C.; Kent, A.; Domenico, A. C.; Bloch-Zupan, A.; Cornel, M.; DeLozier, C.; Farndon, P.; Goetz, P.; Hongson, S.; Houge, G.; Hulten, M.; Kosztolanyi, G.; Kucinskas, V.; Ozcelik, T.; Serqueiros, J.; Soller, M.; Tranebjaerg, L. (Nature Publishing Group, 2010)
      The use of genetics and genomics within a wide range of health-care settings requires health professionals to develop expertise to practise appropriately. There is a need for a common minimum standard of competence in ...
    • Integrating biological pathways and genomic profiles with ChiBE 2 

      Babur, O.; Dogrusoz, U.; Çakır, M.; Aksoy, B. A.; Schultz, N.; Sander, C.; Demir, E. (BioMed Central Ltd., 2014)
      Background: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets.Results: ChiBE is a free, open-source software tool for visualizing, ...
    • Is Romeo dead? On the persistence of organisms 

      Tzinman, R. (Springer Netherlands, 2018)
      According to a prominent view of organism persistence (“vitalicism”), organisms cease to exist at death. According to a rival view (“somaticism”), organisms can continue to exist as dead organisms. Most of the arguments ...
    • Kronecker-based infinite level-dependent QBD processes 

      Dayar, T.; Orhan, M. C. (Applied Probability Trust, 2012)
      Markovian systems with multiple interacting subsystems under the influence of a control unit are considered. The state spaces of the subsystems are countably infinite, whereas that of the control unit is finite. A recent ...
    • Kronecker-based infinite level-dependent QBDS : matrix analytic solution versus simulation 

      Orhan, Muhsin Can (Bilkent University, 2011)
      Markovian systems with multiple interacting subsystems under the influence of a control unit are considered. The state spaces of the subsystems are countably in- finite, whereas that of the control unit is finite. A ...
    • Methods and tools for visualization and management of SBGN process description maps 

      Sarı, Mecit (Bilkent University, 2014)
      Graphs are commonly used to model relational information in many areas such as relational databases, software engineering, biological and social networks. In visualization of graphs, automatic layout, interactive editing ...
    • Moral mechanisms 

      Davenport, D. (2012)
      Moral philosophies are arguably all anthropocentric and so fundamentally concerned with biological mechanisms. Computationalism, on the other hand, sees biology as just one possible implementation medium. Can non-human, ...
    • Polymer-free nanofibers from vanillin/cyclodextrin inclusion complexes: high thermal stability, enhanced solubility and antioxidant property 

      Celebioglu A.; Kayaci-Senirmak, F.; Ipek, S.; Durgun, E.; Uyar T. (Royal Society of Chemistry, 2016)
      Vanillin/cyclodextrin inclusion complex nanofibers (vanillin/CD-IC NFs) were successfully obtained from three modified CD types (HPβCD, HPγCD and MβCD) in three different solvent systems (water, DMF and DMAc) via an ...
    • A privacy-preserving solution for compressed storage and selective retrieval of genomic data 

      Huang Z.; Ayday, E.; Lin, H.; Aiyar, R. S.; Molyneaux, A.; Xu, Z.; Fellay, J.; Steinmetz, L. M.; Hubaux, Jean-Pierre (Cold Spring Harbor Laboratory Press, 2016)
      In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference ...
    • Software support for SBGN maps: SBGN-ML and LibSBGN 

      Iersel, Martijn P. van; Villéger, A. C.; Czauderna, T.; Boyd, S. E.; Bergmann, F. T.; Luna, A.; Demir, E.; Sorokin, A.; Dogrusoz, U.; Matsuoka, Y.; Funahashi, A.; Aladjem, M. I.; Mi, H.; Moodie, S. L.; Kitano, H.; Le novère, N.; Schreiber, F. (Oxford University Press, 2012)
      Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) ...
    • Software tools for visual analysis of cancer genomics data in the context of pathways 

      Bahçeci, İstemi Rahman (Bilkent University, 2016-09)
      Information visualization is concerned with effective visual presentation of abstract information, which reinforces human cognition. Graphs are structures that are well suited to represent relational information. Graph ...
    • The systems biology graphical notation 

      Le Novère, N.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, E.; Wegner, K.; Aladjem, M. I.; Wimalaratne, S. M.; Bergman, F. T.; Gauges, R.; Ghazal, P.; Kawaji, H.; Li, L.; Matsuoka, Y.; Villéger, A.; Boyd, S. E.; Calzone, L.; Courtot, M.; Dogrusoz, U.; Freeman, T. C.; Funahashi, A.; Ghosh, S.; Jouraku, A.; Kim, S.; Kolpakov, F.; Luna, A.; Sahle, S.; Schmidt, E.; Watterson, S.; Wu, G.; Goryanin, I.; Kell, D. B.; Sander, C.; Sauro, H.; Snoep, J. L.; Kohn, K.; Kitano, H. (Nature Publishing Group, 2009-08)
      Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for ...
    • Time-delay estimation in multiple-input single-output systems 

      Kocak F.; Gezici, S. (2010)
      In this paper, the time-delay estimation problem is studied for multiple-input single-output (MISO) systems. First, a theoretical analysis is carried out by deriving the Cramer-Rao lower bound (CRLB) for time-delay estimation ...