Browsing by Keywords "Software"

Now showing items 1-20 of 23

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

      Doğrusöz, Uğur; Çetintaş, Ahmet; Demir, Emek; Babur, Özgün (BioMed Central Ltd., 2009-11-16)
      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, Emek; 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, Özgün; 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.; Doğrusöz, Uğur; 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, 2010-09)
      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, Özgün; Doğrusöz, Uğur; Demir, Emek; Sander, C. (Oxford University Press, 2010-02-01)
      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, Uğur; Ulusoy, Özgür; Çetin, A. Enis (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 ...

    • GenASM: a high-performance, low-power approximate string matching acceleration framework for genome sequence analysis 

      Şenol-Çalı, D.; Kalsi, G. S.; Bingöl, Zülal; Fırtına, C.; Subramanian, L.; Kim, J. S.; Ausavarungnirun, R.; Alser, M.; Gomez-Luna, J.; Boroumand, A.; Norion, A.; Scibisz, A.; Subramoneyon, S.; Alkan, Can; Ghose, S.; Mutlu, Onur (IEEE Computer Society, 2020)
      Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. To perform genome sequencing, devices extract ...

    • 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. Enis (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, Koray D.; Karakülah, G.; Yakıcıer, Cengiz M.; Acar, Aybar C.; Konu, Özlen (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, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Ayaz, Aslı; Güleşır, Gürcan; Nişancı, Gürkan; Çetin Atalay, Rengül (Oxford University Press, 2004-02-12)
      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 ...

    • PAMOGK-Web: a framework for cancer subtype identification using copy number variatıons 

      Akdemir, Furkan Mustafa (Bilkent University, 2020-12)
      Detection of molecular sub-groups of cancer is important for developing cancer therapeutics and to understand the underlying causes of the molecular differences in these groups. The cancer sequencing projects made multi-omics ...

    • PATIKAmad: putting microarray data into pathway context 

      Babur, Özgün; Colak, Recep; Demir, Emek; Doğrusöz, Uğur (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 

      Doğrusöz, Uğur; Erson, E. Zeynep; Giral, Erhan; Demir, Emek; Babur, Özgün; Çetintaş, Ahmet; Çolak, Recep (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 ...

    • Robust inference of kinase activity using functional networks 

      Yılmaz, S.; Ayati, M.; Schlatzer, D.; Çiçek, A. Ercüment (Nature Publishing Group, 2021-02-19)
      Mass spectrometry enables high-throughput screening of phosphoproteins across a broad range of biological contexts. When complemented by computational algorithms, phospho-proteomic data allows the inference of kinase ...

    • 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) ...

    • SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more 

      Balcı, Hakan; Doğrusöz, Uğur; Özgül, Yusuf Ziya; Atayev, Perman (Public Library of Science, 2022-11-14)
      Visualization is a key recurring requirement for effective analysis of relational data. Biology is no exception. It is imperative to annotate and render biological models in standard, widely accepted formats. Finding ...