Now showing items 1-9 of 9

    • 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 ...
    • The BioPAX community standard for pathway data sharing 

      Demir, E.; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Ö.; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Dogrusoz, U.; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D. (Nature Publishing Group, 2010)
      Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway ...
    • Cellular internalization of therapeutic oligonucleotides by peptide amphiphile nanofibers and nanospheres 

      Mumcuoglu, D.; S. Ekiz, M.; Gunay, G.; Tekinay, T.; Tekinay, A. B.; Guler, M. O. (American Chemical Society, 2016-04)
      Oligonucleotides are promising drug candidates due to the exceptionally high specificity they exhibit toward their target DNA and RNA sequences. However, their poor pharmacokinetic and pharmacodynamic properties, in ...
    • Community-driven roadmap for integrated disease maps 

      Ostaszewski, M.; Gebel, S.; Kuperstein, I.; Mazein, A.; Zinovyev, A.; Dogrusoz, U.; Hasenauer, J.; Fleming, R. M. T.; Novere, N. L.; Gawron, P.; Ligon, T.; Niarakis, A.; Nickerson, D.; Weindl, D.; Balling, R.; Barillot, E.; Auffray, C.; Schneider, R. (Oxford University Press, 2018)
      The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and ...
    • Deepside: predicting drug side effects with deep learning 

      Üner, Onur Can (Bilkent University, 2019-10)
      Drug failures due to unforeseen adverse effects at clinical trials pose health risks for the participants and cause substantial financial losses. Side effect prediction algorithms, on the other hand, have the potential ...
    • Hybridization of fano and vibrational resonances in surface-enhanced infrared absorption spectroscopy of streptavidin monolayers on metamaterial substrates 

      Alici, K. B. (2014)
      We present spectral hybridization of organic and inorganic resonant materials and related bio-sensing mechanism. We utilized a bound protein (streptavidin) and a Fano-resonant metasurface to illustrate the concept. The ...
    • Subsequence-based feature map for protein function classification 

      Sarac, O. S.; Gürsoy-Yüzügüllü, O.; Cetin Atalay, R.; Atalay, V. (Elsevier, 2008)
      Automated classification of proteins is indispensable for further in vivo investigation of excessive number of unknown sequences generated by large scale molecular biology techniques. This study describes a discriminative ...
    • 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 ...
    • Transmission Near-Field Scanning Optical Microscopy Investigation on Cellular Uptake Behavior of Iron Oxide Nanoparticles 

      Zhang, Y.; Kyle J.R.; Penchev, M.; Yazdanpanah V.; Yu J.; Li, Y.; Yang, M.; Budak G.; Özbay, Ekmel; Ozkan, M.; Ozkan, C.S. (2012)
      Cellular uptake behavior of iron oxide nanoparticles is investigated using a transmission near-field scanning optical microscopy (NSOM) without the need of fluorescent labeling. By using the transmission NSOM system, we ...