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TailFindR: Alignmentfree poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing
(Peer reviewed; Journal article, 20190702)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 genomewide ... 
Techniques in parameterized algorithm design
(Doctoral thesis, 20060306)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, 200810)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 casebased, checking a likely ... 
ThermoRawFileParser: Modular, Scalable, and CrossPlatform 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 edgeweighted 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 NPhard ... 
Three problems on wellpartitioned chordal graphs
(Journal article; Peer reviewed, 2021)In this work, we solve three problems on wellpartitioned chordal graphs. First, we show that every connected (resp., 2connected) wellpartitioned chordal graph has a vertex that intersects all longest paths (resp., longest ... 
Throughput and robustness of bioinformatics pipelines for genomescale data analysis
(Doctoral thesis, 20140219)The postgenomic era has been heavily influenced by the rapid development of highthroughput molecularscreening technologies, which has enabled genomewide analysis approaches on an unprecedented scale. The constantly ... 
Tight bounds for parameterized complexity of Cluster Editing
(Conference object; 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 ... 
TMM@: a web application for the analysis of transmembrane helix mobility
(Peer reviewed; Journal article, 20070702)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, 20151103)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 SkeinTheoretic Aspects of Braided Fusion Categories
(Doctoral thesis, 20210827)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 ... 
Tournaments and Optimality: New Results in Parameterized Complexity
(Doctoral thesis; Peer reviewed, 20131122) 
Towards a deeper understanding of APN functions and related longstanding problems
(Doctoral thesis, 20210824)This dissertation is dedicated to the properties, construction and analysis of APN and AB functions. Being cryptographically optimal, these functions lack any general structure or patterns, which makes their study very ... 
Towards a multilevel model transformation engine
(Master thesis, 2017)Domain specific modelling languages (DSML) are usually defined through fixed level meta modelling tools such as EMF. While this is sufficient for defining languages that has no overlap with other languages, the approach ... 
Towards a Polynomial Kernel for Directed Feedback Vertex Set
(Journal article; Peer reviewed, 2020)In the DIRECTED FEEDBACK VERTEX SET (DFVS) problem, the input is a directed graph D and an integer k. The objective is to determine whether there exists a set of at most k vertices intersecting every directed cycle of D. ... 
Towards a Secure Framework for mHealth. A Case Study in Mobile Data Collection Systems
(Doctoral thesis, 20151105)The rapid growth in the mobile communications technology and wide cellular coverage created an opportunity to satisfy the demand for lowcost health care solutions. Mobile Health (a.k.a. mHealth) is a promising health ... 
Towards a SpreadsheetBased Language Workbench
(Chapter, 2021)Spreadsheets are widely used across industries for various purposes, including for storing and manipulating data in a structured form. Such structured forms—expressed using tabular notation—have found their way in language ... 
Towards Advanced Interactive Visualization for Virtual Atlases
(Advances in Experimental Medicine and Biology, Chapter; Peer reviewed, 2019)An atlas is generally defined as a bound collection of tables, charts or illustrations describing a phenomenon. In an anatomical atlas for example, a collection of representative illustrations and text describes anatomy ... 
(Towards an) Implementation of a Graphical Editor for Diagrammatic Predicate Logic in the Eclipse Platform
(Master thesis, 2008)The primary goal of this master's thesis is to explore how the Eclipse Platform can be beneficial for the Generic Diagrammatic Software Specification project, and how a graphical editor in the Eclipse Platform can be put ...