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 ...
    • 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 ...
    • BRAPH: A graph theory software for the analysis of brain connectivity 

      Mijalkov, M.; Kakaei, E.; Pereira, J. B.; Westman, E.; Volpe, G. (Public Library of Science, 2017)
      The brain is a large-scale complex network whose workings rely on the interaction between its various regions. In the past few years, the organization of the human brain network has been studied extensively using concepts ...
    • 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 ...
    • Content-based retrieval of historical Ottoman documents stored as textual images 

      Şaykol, E.; Sinop, A. K.; Güdükbay U.; Ulusoy, Ö.; Çetin, A. E. (IEEE, 2004)
      There is an accelerating demand to access the visual content of documents stored in historical and cultural archives. Availability of electronic imaging tools and effective image processing techniques makes it feasible to ...
    • EVIM: a software package for extreme value analysis in MATLAB 

      Gençay, R.; Selçuk, F.; Ulugülyagci, A. (Walter de Gruyter GmbH, 2001)
      From the practitioners' point of view, one of the most interesting questions that tail studies can answer is what are the extreme movements that can be expected in financial markets? Have we already seen the largest ones ...
    • Identification of relative protein bands in polyacrylamide gel electrophoresis (PAGE) using a multi-resolution snake algorithm 

      Gürcan, M. N.; Koyutürk, M.; Yildiz, H. S.; Çetin-Atalay R.; Çetin, A. E. (Informa Healthcare, 1999-06)
      In polyacrylamide gel electrophoresis (PAGE) image analysis, it is important to determine the percentage of the protein of interest of a protein mixture. This study presents reliable computer software to determine this ...
    • Inference attacks against kin genomic privacy 

      Ayday, E.; Humbert M. (Institute of Electrical and Electronics Engineers Inc., 2017)
      Genomic data poses serious interdependent risks: your data might also leak information about your family members' data. Methods attackers use to infer genomic information, as well as recent proposals for enhancing genomic ...
    • 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, ...
    • Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal 

      Gao J.; Aksoy, B. A.; Dogrusoz, U.; Dresdner, G.; Gross, B.; Sumer, S. O.; Sun, Y.; Jacobsen, A.; Sinha, R.; Larsson, E.; Cerami, E.; Sander, C.; Schultz, N. (American Association for the Advancement of Science (A A A S), 2013)
      The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer ...
    • MESAdb: microRNA expression and sequence analysis database 

      Kaya, K. D.; Karakülah, G.; Yakıcıer, C. M.; Acar, A. C.; Konu, Ö. (Oxford University Press, 2011)
      MicroRNA expression and sequence analysis database (http://konulab.fen. bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple ...
    • mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications 

      Hach, F.; Sarrafi, I.; Hormozdiari, F.; Alkan C.; Eichler, E. E.; Sahinalp, S. C. (Oxford University Press, 2014)
      High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide ...
    • An ontology for collaborative construction and analysis of cellular pathways 

      Demir, E.; Babur, O.; Dogrusoz, U.; Gursoy, A.; Ayaz, A.; Gulesir, G.; Nisanci, G.; Atalay, R. C. (Oxford University Press, 2004)
      Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an ...
    • PATIKAmad: putting microarray data into pathway context 

      Babur, O.; Colak, R.; Demir, E.; Dogrusoz, U. (Wiley - V C H Verlag GmbH & Co. KGaA, 2008-06)
      High-throughput experiments, most significantly DNA microarrays, provide us with system-scale profiles. Connecting these data with existing biological networks poses a formidable challenge to uncover facts about a cell's ...
    • PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization 

      Dogrusoz, U.; Erson, E. Z.; Giral, E.; Demir, E.; Babur, O.; Cetintas, A.; Colak, R. (Oxford University Press, 2006-02-01)
      Summary: PATIKAweb provides a Web interface for retrieving and analyzing biological pathways in the PATIKA database, which contains data integrated from various prominent public pathway databases. It features a user-friendly ...
    • 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) ...
    • 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 ...
    • VISIBIOweb: visualization and layout services for BioPAX pathway models 

      Dilek, A.; Belviranli, M. E.; Dogrusoz, U. (Oxford University Press, 2010-05)
      With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; ...