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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 ... 
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 kcreature as an induced subgraph or a kskinnyladder ... 
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
(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 populationbased 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, 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 ... 
Total dominator chromatic number of ksubdivision 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) ... 
Tournaments and Optimality: New Results in Parameterized Complexity
(Doctoral thesis, 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 ...