Browsing by Keywords "Bioinformatics"

Now showing items 1-20 of 25

    • 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 ...

    • Analyzing causal relationships in proteomic profiles using CausalPath 

      Luna, A.; Siper, M. C.; Korkut, A.; Durupinar, F.; Aslan, J. E.; Sander, C.; Demir, E.; Babur, O.; Doğrusöz, Uğur (Cell Press, 2021-12-17)
      CausalPath (causalpath.org) evaluates proteomic measurements against prior knowledge of biological pathways and infers causality between changes in measured features, such as global protein and phospho-protein levels. It ...

    • Building and improving reference genome assemblies 

      Steinberg, K. M.; Schneider, V. A.; Alkan, Can; Montague, M. J.; Warren, W. C.; Church, D. M.; Wilson, R. K. (IEEE, 2017-01)
      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, Mohammed; Almadhoun, Nour; Nouri, Azita; Alkan, Can; Ayday, Erman (Springer, 2016-09)
      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 ...

    • Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR−/- mice 

      Hanifehnezhad, A.; Kehribar, Ebru Şahin; Öztop, S.; Sheraz, Ali; Kasırga, Serkan; Ergünay, K.; Önder, S.; Yılmaz, E.; Engin, D.; Oğuzoğlu, T. Ç.; Şeker, Urartu Özgür Şafak; Yılmaz, E.; Özkul, A. (Elsevier, 2020)
      The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently a global pandemic with unprecedented public health, economic and social impact. The development of effective mitigation strategies, therapeutics and ...

    • Examining the annealing schedules for RNA design algorithm 

      Erhan, H. E.; Sav, Sinem; Kalashnikov, S.; Tsang, H. H. (IEEE, 2016-07)
      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 ...

    • 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 ...

    • Improving genome assemblies using multi-platform sequence data 

      Kavak, P.; Ergüner, B.; Üstek, D.; Yüksel, B.; Saǧıroǧlu, M. Ş.; Güngör, T.; Alkan, Can (Springer, 2015-09)
      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, Sinem; Tsang, H. H. (IEEE, 2017-12)
      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. Ercüment (TÜBİTAK, 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 

      Genç, Burkay; Doğrusöz, Uğur (Elsevier, 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 

      Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Civril, Ali; Demir, Emek (Elsevier, 2009-03-15)
      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, 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 ...

    • 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 ...