Now showing items 41-60 of 292

    • Community curation of bioinformatics software and data resources 

      Ison, Jon; Ménager, Hervé; Brancotte, Bryan; Jaaniso, Erik; Salumets, Ahto; Raček, Tomáš; Lamprecht, Anna-Lena; Palmblad, Magnus; Kalaš, Matúš; Chmura, Piotr; Hancock, John M; Schwämmle, Veit; Ienasescu, Hans-Ioan (Peer reviewed; Journal article, 2019)
      The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for ...
    • Community Detection on the GPU 

      Naim, Md.; Manne, Fredrik; Halappanavar, Mahantesh; Tumeo, Antonino (Conference object; Peer reviewed, 2017)
      We present and evaluate a new GPU algorithm based on the Louvain method for community detection. Our algorithm is the first for this problem that parallelizes the access to individual edges. In this way we can fine tune ...
    • Community-driven development for computational biology at Sprints, Hackathons and Codefests 

      Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul J. P.; Booth, Timothy; Chilton, John; Cock, Peter J. A.; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R.; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J.; Guimera, Roman V.; Katayama, Toshiaki; Chapman, Brad A. (Peer reviewed; Journal article, 2014-11-27)
      Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ...
    • A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver 

      Zhang, Xiaokang; Jonassen, Inge (Chapter; Conference object; Peer reviewed, 2019)
      Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its ...
    • Comparative Visualization of Protein Secondary Structures 

      Kocincova, Lucia; Jaresova, Miroslava; Byska, Jan; Parulek, Julius; Hauser, Helwig; Kozlikova, Barbora (Peer reviewed; Journal article, 2017-02-15)
      Background: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein ...
    • Comparison of Discrete and Continuous Models for the Pooling Problem 

      Alfaki, Mohammed; Haugland, Dag (Chapter; Peer reviewed, 2011)
      The pooling problem is an important global optimization problem which is encountered in many industrial settings. It is traditionally modeled as a bilinear, nonconvex optimization problem, and solved by branch-and-bound ...
    • A complexity dichotomy for critical values of the b-chromatic number of graphs 

      Jaffke, Lars; Lima, Paloma T. (Peer reviewed; Journal article, 2019-08-20)
      A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has ...
    • A complexity dichotomy for critical values of the b-chromatic number of graphs 

      Lima, Paloma T.; Jaffke, Lars (Journal article; Peer reviewed, 2020)
      A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has ...
    • Complexity of the Steiner Network Problem with Respect to the Number of Terminals 

      Eiben, Eduard; Knop, Dusan; Panolan, Fahad; Suchý, Ondřej (Journal article; Peer reviewed, 2019)
      In the Directed Steiner Network problem we are given an arc-weighted digraph G, a set of terminals T subseteq V(G) with |T|=q, and an (unweighted) directed request graph R with V(R)=T. Our task is to output a subgraph H ...
    • Computational science in the eighteenth century. Test cases for the methods of Newton, Raphson, and Halley: 1685 to 1745 

      Steihaug, Trond (Peer reviewed; Journal article, 2020)
      This is an overview of examples and problems posed in the late 1600s up to the mid 1700s for the purpose of testing or explaining the two different implementations of the Newton-Raphson method, Newton’s method as described ...
    • Computing cutwidth and pathwidth of semi-complete digraphs via degree orderings 

      Pilipczuk, Michal Pawel (Conference object; Peer reviewed; Journal article, 2013)
      The notions of cutwidth and pathwidth of digraphs play a central role in the containment theory for tournaments, or more generally semi-complete digraphs, developed in a recent series of papers by Chudnovsky, Fradkin, Kim, ...
    • Connecting the Dots (with Minimum Crossings) 

      Agrawal, Akanksha; Guspiel, Grzegorz; Madathil, Jayakrishnan; Saurabh, Saket; Zehavi, Meirav (Journal article; Peer reviewed, 2019)
      We study a prototype Crossing Minimization problem, defined as follows. Let F be an infinite family of (possibly vertex-labeled) graphs. Then, given a set P of (possibly labeled) n points in the Euclidean plane, a collection ...
    • Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival 

      Sokolowski, Bernd; Orchard, Sandra; Harvey, Margaret; Sridhar, Settu; Sakai, Yoshihisa (Peer reviewed; Journal article, 2011-12-09)
      The large-conductance Ca2+-activated K+ (BK) channel and its b-subunit underlie tuning in non-mammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and ...
    • Constructing APN functions through isotopic shifts 

      Budaghyan, Lilya; Calderini, Marco; Carlet, Claude; Coulter, Robert; Villa, Irene (Journal article; Peer reviewed, 2020)
      Almost perfect nonlinear (APN) functions over fields of characteristic 2 play an important role in cryptography, coding theory and, more generally, mathematics and information theory. In this paper we deduce a new method ...
    • Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization 

      Parulek, Julius; Jönsson, Daniel; Ropinski, Timo; Bruckner, Stefan; Ynnerman, Anders; Viola, Ivan (Peer reviewed; Journal article, 2014-05-06)
      Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the ...
    • Covering Vectors by Spaces in Perturbed Graphic Matroids and Their Duals 

      Fomin, Fedor; Golovach, Petr; Lokshtanov, Daniel; Saurabh, Saket; Zehavi, Meirav (Peer reviewed; Journal article, 2019)
      Perturbed graphic matroids are binary matroids that can be obtained from a graphic matroid by adding a noise of small rank. More precisely, an r-rank perturbed graphic matroid M is a binary matroid that can be represented ...
    • Current Trends for 4D Space-Time Topology for Semantic Flow Segmentation 

      Matković, Krešimir; Lež, Alan; Hauser, Helwig; Pobitzer, Armin; Theisel, Holger; Kuhn, Alexander; Otto, Mathias; Peikert, Ronald; Schindler, Benjamin; Fuchs, Raphael (Peer reviewed; Journal article, 2011)
    • Curve Density Estimates 

      Lampe, Ove Daae; Hauser, Helwig (Peer reviewed; Journal article, 2011-06-28)
      In this work, we present a technique based on kernel density estimation for rendering smooth curves. With this approach, we produce uncluttered and expressive pictures, revealing frequency information about one, or, multiple ...
    • Curve-Centric Volume Reformation for Comparative Visualization 

      Lampe, Ove Daae; Correa, Carlos; Ma, Kwan-Liu; Hauser, Helwig (Peer reviewed; Journal article, 2009-10-11)
      We present two visualization techniques for curve-centric volume reformation with the aim to create compelling comparative visualizations. A curve-centric volume reformation deforms a volume, with regards to a curve in ...
    • Cyclability in Graph Classes 

      Crespelle, Christophe Dominique; Feghali, Carl; Golovach, Petr (Peer reviewed; Journal article, 2019)
      A subset T subseteq V(G) of vertices of a graph G is said to be cyclable if G has a cycle C containing every vertex of T, and for a positive integer k, a graph G is k-cyclable if every subset of vertices of G of size at ...