• Co-Degeneracy and Co-Treewidth: Using the Complement to Solve Dense Instances 

      Duarte, Gabriel; Oliveira, Mateus De Oliveira; Souza, Uéverton S. (Journal article; Peer reviewed, 2021)
      Clique-width and treewidth are two of the most important and useful graph parameters, and several problems can be solved efficiently when restricted to graphs of bounded clique-width or treewidth. Bounded treewidth implies ...
    • Coherence for Monoidal Groupoids in HoTT 

      Piceghello, Stefano (Journal article; Peer reviewed, 2020)
      We present a proof of coherence for monoidal groupoids in homotopy type theory. An important role in the formulation and in the proof of coherence is played by groupoids with a free monoidal structure; these can be represented ...
    • Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication 

      Mitternacht, Simon; Berezovsky, Igor N. (Peer reviewed; Journal article, 2011-12-08)
      Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited ...
    • Combining Aspect-Oriented and Strategic Programming 

      Kalleberg, Karl Trygve; Visser, Eelco (Peer reviewed; Journal article, 2006-01)
      Properties such as logging, persistence, debugging, tracing, distribution, performance monitoring and exception handling occur in most programming paradigms and are normally very difficult or even impossible to modularizewith ...
    • 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 (Chapter; 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 (Communications in Computer and Information Science; 1056, Chapter; 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 between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast 

      Ludl, Adriaan-Alexander; Michoel, Tom Luk Robert (Journal article; Peer reviewed, 2021)
      Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a ...
    • 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 

      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 ...
    • 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 ...
    • 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 ...
    • Composition of multilevel domain-specific modelling languages 

      Rodríguez, Alejandro; Macias Gomez de Villar, Fernando; Durán, Francisco; Rutle, Adrian; Wolter, Uwe Egbert (Journal article; Peer reviewed, 2023)
      Multilevel Modelling (MLM) approaches make it possible for designers and modellers to work with an unlimited number of abstraction levels to specify their domain-specific modelling languages (DSMLs). To fully exploit MLM ...
    • Compressing permutation groups into grammars and polytopes. A graph embedding approach 

      Jaffke, Lars; De Oliveira Oliveira, Mateus; Tiwary, Hans Raj (Journal article; Peer reviewed, 2020)
      It can be shown that each permutation group G ⊑ 𝕊_n can be embedded, in a well defined sense, in a connected graph with O(n+|G|) vertices. Some groups, however, require much fewer vertices. For instance, 𝕊_n itself can ...
    • Computational complexity aspects of super domination 

      Bujtás, Csilla; Ghanbari, Nima; Klavžar, Sandi (Journal article; Peer reviewed, 2023)
      Let G be a graph. A dominating set D ⊆ V (G) is a super dominating set if for every vertex x ∈ V (G) \ D there exists y ∈ D such that NG (y) ∩ (V (G) \ D)) = {x}. The cardinality of a smallest super dominating set of G is ...
    • 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 (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 ...