Browsing Department of Informatics by Title
Now showing items 820-839 of 925
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A survey of parameterized algorithms and the complexity of edge modification
(Journal article; Peer reviewed, 2023)The survey is a comprehensive overview of the developing area of parameterized algorithms for graph modification problems. It describes state of the art in kernelization, subexponential algorithms, and parameterized ... -
Sustainability in mining protocols for public blockchains
(Master thesis, 2019-05-04)Blockchains are a somewhat new technology with much potential and it is meeting growing public interest. However, with wider use of the technology we face the challenge of sustainability since the current mining protocols ... -
Synthesis and Analysis of Petri Nets from Causal Specifications
(Journal article; Peer reviewed, 2022)Petri nets are one of the most prominent system-level formalisms for the specification of causality in concurrent, distributed, or multi-agent systems. This formalism is abstract enough to be analyzed using theoretical ... -
Systematic exploration of error sources in pyrosequencing flowgram data
(Peer reviewed; Journal article, 2011)Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several ... -
TailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing
(Peer reviewed; Journal article, 2019-07-02)Polyadenylation at the 3′-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide ... -
Taming Graphs with No Large Creatures and Skinny Ladders
(Journal article; Peer reviewed, 2022)We confirm a conjecture of Gartland and Lokshtanov [arXiv:2007.08761]: if for a hereditary graph class 𝒢 there exists a constant k such that no member of 𝒢 contains a k-creature as an induced subgraph or a k-skinny-ladder ... -
Targeting performance and user-friendliness: GPU-accelerated finite element computation with automated code generation in FEniCS
(Journal article; Peer reviewed, 2023)This paper studies the use of automated code generation to provide user-friendly GPU acceleration for solving partial differential equations (PDEs) with finite element methods. By extending the FEniCS framework and its ... -
Techniques in parameterized algorithm design
(Doctoral thesis, 2006-03-06)In this thesis we give a novel classification of techniques for designing parameterized algorithms, together with research publications applying these techniques, in particular Crown Decompositions, to various problems. ... -
Ten Open Challenges in Medical Visualization
(Journal article; Peer reviewed, 2021)The medical domain has been an inspiring application area in visualization research for many years already, but many open challenges remain. The driving forces of medical visualization research have been strengthened by ... -
Testing with Concepts and Axioms in C++
(Reports in Informatics: 368, Research report, 2008-10)Modern development practices encourage extensive testing of code while it is still under development, using unit tests to check individual code units in isolation. Such tests are typically case-based, checking a likely ... -
ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion
(Journal article; Peer reviewed, 2020)The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical ... -
Three Is Enough for Steiner Trees
(Journal article; Peer reviewed, 2021)In the Steiner tree problem, the input consists of an edge-weighted graph G together with a set S of terminal vertices. The goal is to find a minimum weight tree in G that spans all terminals. This fundamental NP-hard ... -
Three problems on well-partitioned chordal graphs
(Journal article; Peer reviewed, 2021)In this work, we solve three problems on well-partitioned chordal graphs. First, we show that every connected (resp., 2-connected) well-partitioned chordal graph has a vertex that intersects all longest paths (resp., longest ... -
Throughput and robustness of bioinformatics pipelines for genome-scale data analysis
(Doctoral thesis, 2014-02-19)The post-genomic era has been heavily influenced by the rapid development of highthroughput molecular-screening technologies, which has enabled genome-wide analysis approaches on an unprecedented scale. The constantly ... -
Tight bounds for parameterized complexity of Cluster Editing
(Peer reviewed; Journal article, 2013)In the Correlation Clustering problem, also known as Cluster Editing, we are given an undirected graph G and a positive integer k; the task is to decide whether G can be transformed into a cluster graph, i.e., a disjoint ... -
The timing of pregnancies after bariatric surgery has no impact on children’s health—a nationwide population-based registry analysis
(Journal article; Peer reviewed, 2023)Purpose Bariatric surgery has a favorable effect on fertility in women. However, due to a lack of data regarding children’s outcomes, the ideal time for conception following bariatric surgery is unknown. Current guidelines ... -
TMM@: a web application for the analysis of transmembrane helix mobility
(Peer reviewed; Journal article, 2007-07-02)Background: To understand the mechanism by which a protein transmits a signal through the cell membrane, an understanding of the flexibility of its transmembrane (TM) region is essential. Normal Mode Analysis (NMA) has ... -
Tools and data services registry: a community effort to document bioinformatics resources
(Peer reviewed; Journal article, 2015-11-03)Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools ... -
Topological Quantum and Skein-Theoretic Aspects of Braided Fusion Categories
(Doctoral thesis, 2021-08-27)The first part of this thesis is dedicated to the study of anyons and exchange symmetry. We discuss the theory of identical particles and recap the standard algebraic framework for describing the exchange statistics of ... -
Total dominator chromatic number of k-subdivision of graphs
(Journal article, 2023)Let G be a simple graph. A total dominator coloring of G, is a proper coloring of the vertices of G in which each vertex of the graph is adjacent to every vertex of some color class. The total dominator chromatic (TDC) ...