Now showing items 1-20 of 22

    • 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 ...
    • 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 ...
    • Can you really anonymize the donors of genomic data in today’s digital world? 

      Alser, M.; Almadhoun, N.; Nouri, A.; Alkan C.; Ayday, E. (Springer Verlag, 2016)
      The rapid progress in genome sequencing technologies leads to availability of high amounts of genomic data. Accelerating the pace of biomedical breakthroughs and discoveries necessitates not only collecting millions of ...
    • Examining the annealing schedules for RNA design algorithm 

      Erhan, H. E.; Sav, S.; Kalashnikov, S.; Tsang, H. H. (Institute of Electrical and Electronics Engineers, 2016)
      RNA structures are important for many biological processes in the cell. One important function of RNA are as catalytic elements. Ribozymes are RNA sequences that fold to form active structures that catalyze important ...
    • A framework for management of multiple views of cellular pathway graphs 

      Güleşir, Gürcan (Bilkent University, 2003)
      The enhancements in genomic studies have given birth to the necessity of advanced techniques for storing, integrating and analyzing the accumulated data regarding molecular level cellular processes. Since this data is ...
    • Improving genome assemblies using multi-platform sequence data 

      Kavak, P.; Ergüner, B.; Üstek, D.; Yüksel, B.; Saǧıroǧlu, M. Ş.; Güngör, T.; Alkan C. (Springer Verlag, 2016)
      Accurate de novo assembly using short reads generated by next generation sequencing technologies is still an open problem. Although there are several assembly algorithms developed for data generated with different sequencing ...
    • Integrating biological pathways and genomic profiles with ChiBE 2 

      Çakır, Merve (Bilkent University, 2013)
      Biological pathways store information about spatial and temporal organization of interactions taking place in an organism. They hold valuable information that can assist scientific community in understanding the details ...
    • 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 ...
    • Investigation of multi-objective optimization criteria for RNA design 

      Hampson, D. J. D.; Sav, S.; Tsang, H. H. (Institute of Electrical and Electronics Engineers, 2017)
      RNA design is the inverse of RNA folding and it appears to be NP-hard. In RNA design, a secondary structure is given and the goal is to find a nucleotide sequence that will fold into this structure. To find such sequence(s) ...
    • k-Shell decomposition reveals structural properties of the gene coexpression network for neurodevelopment 

      Çiçek, A. E. (Scientific and Technical Research Council of Turkey, 2017)
      Neurodevelopment is a dynamic and complex process, which involves interactions of thousands of genes. Understanding the mechanisms of brain development is important for uncovering the genetic architectures of neurodevelopmental ...
    • A layout algorithm for signaling pathways 

      Genc, B.; Dogrusoz, U. (Elsevier Inc., 2006-01-20)
      Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. ...
    • A layout algorithm for undirected compound graphs 

      Dogrusoz, U.; Giral, E.; Cetintas, A.; Civril, A.; Demir, E. (Elsevier Inc., 2009-03)
      We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout ...
    • 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 ...
    • An ontology for computer-aided modeling of cellular processes 

      Emek, Demir (Bilkent University, 2005-10)
      Cellular processes form the hardware layer of living organisms. Malfunctions in cellular processes are responsible for most of the currently incurable diseases. Not surprisingly, knowledge about cellular processes are ...
    • Patika Web : a Web service for accessing and visualizing pathway data in patika database 

      Erson, Emine Zeynep (Bilkent University, 2005)
      After completion of Human Genome Project, there has been an exponential increase in the available biological data. Although there has been an enormous effort for creating ontologies, standards and tools, current ...
    • 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 ...
    • 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 ...
    • Selective replicated declustering for arbitrary queries 

      Oktay, K. Yasin; Türk, Ata; Aykanat, Cevdet (Springer, 2009-08)
      Data declustering is used to minimize query response times in data intensive applications. In this technique, query retrieval process is parallelized by distributing the data among several disks and it is useful in ...
    • SIMARD: a simulated annealing based RNA design algorithm with quality pre-selection strategies 

      Sav, S.; Hampson, D. J. D.; Tsang, H. H. (Institute of Electrical and Electronics Engineers Inc., 2017)
      Most of the biological processes including expression levels of genes and translation of DNA to produce proteins within cells depend on RNA sequences, and the structure of the RNA plays vital role for its function. RNA ...
    • 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 ...