Browsing Department of Informatics by Document Types "Journal article"
Now showing items 4160 of 315

Close Relatives of Feedback Vertex Set Without SingleExponential Algorithms Parameterized by Treewidth
(Journal article; Peer reviewed, 2020)The Cut & Count technique and the rankbased approach have lead to singleexponential FPT algorithms parameterized by treewidth, that is, running in time 2^𝒪(tw)n^𝒪(1), for Feedback Vertex Set and connected versions of ... 
Clustering to Given Connectivities
(Peer reviewed; Journal article, 2019)We define a general variant of the graph clustering problem where the criterion of density for the clusters is (high) connectivity. In Clustering to Given Connectivities, we are given an nvertex graph G, an integer k, and ... 
Coherence for Monoidal Groupoids in HoTT
(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
(Peer reviewed; Journal article, 20111208)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 AspectOriented and Strategic Programming
(Peer reviewed; Journal article, 200601)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
(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 ... 
Communitydriven development for computational biology at Sprints, Hackathons and Codefests
(Peer reviewed; Journal article, 20141127)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 ... 
Comparative Visualization of Protein Secondary Structures
(Peer reviewed; Journal article, 20170215)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 mediationbased methods for reconstructing causal gene networks in yeast
(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 ... 
A complexity dichotomy for critical values of the bchromatic number of graphs
(Journal article; Peer reviewed, 2020)A bcoloring 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 bColoring problem asks whether a graph G has ... 
A complexity dichotomy for critical values of the bchromatic number of graphs
(Peer reviewed; Journal article, 20190820)A bcoloring 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 bColoring problem asks whether a graph G has ... 
Complexity of the Steiner Network Problem with Respect to the Number of Terminals
(Journal article; Peer reviewed, 2019)In the Directed Steiner Network problem we are given an arcweighted 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 ... 
Compressing permutation groups into grammars and polytopes. A graph embedding approach
(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 science in the eighteenth century. Test cases for the methods of Newton, Raphson, and Halley: 1685 to 1745
(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 NewtonRaphson method, Newton’s method as described ... 
Computing cutwidth and pathwidth of semicomplete digraphs via degree orderings
(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 semicomplete digraphs, developed in a recent series of papers by Chudnovsky, Fradkin, Kim, ... 
Computing minimal triangulation in Time o(n^2.376)
(Journal article, 2005) 
Connecting the Dots (with Minimum Crossings)
(Journal article; Peer reviewed, 2019)We study a prototype Crossing Minimization problem, defined as follows. Let F be an infinite family of (possibly vertexlabeled) graphs. Then, given a set P of (possibly labeled) n points in the Euclidean plane, a collection ... 
Conserved BK ChannelProtein Interactions Reveal Signals Relevant to Cell Death and Survival
(Peer reviewed; Journal article, 20111209)The largeconductance Ca2+activated K+ (BK) channel and its bsubunit underlie tuning in nonmammalian 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
(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 LevelsofDetail and Visual Abstraction for Seamless Molecular Visualization
(Peer reviewed; Journal article, 20140506)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 ...