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Randomised Construction and Dynamic Decoding of LDPC Codes
(Master thesis, 20051130) 
Rank vertex cover as a natural problem for algebraic compression
(Journal article; Peer reviewed, 2019)The question of the existence of a polynomial kernelization of the Vertex Cover Above LP problem was a longstanding, notorious open problem in parameterized complexity. Some years ago, the breakthrough work by Kratsch and ... 
Rapid genome editing by CRISPRCas9POLD3 fusion
(Journal article; Peer reviewed, 2021)Precision CRISPR gene editing relies on the cellular homologydirected DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the ... 
RASflow: an RNASeq analysis workflow with Snakemake
(Journal article; Peer reviewed, 2020)Background With the cost of DNA sequencing decreasing, increasing amounts of RNASeq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNASeq ... 
Rate and power allocation for discreterate link adaptation
(Peer reviewed; Journal article, 20080109)Link adaptation, in particular adaptive coded modulation (ACM), is a promising tool for bandwidthefficient transmission in a fading environment. The main motivation behind employing ACM schemes is to improve the spectral ... 
ReCodLiver0.9: Overcoming Challenges in GenomeScale Metabolic Reconstruction of a Nonmodel Species
(Journal article; Peer reviewed, 202011)The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in ... 
Recognizing Proper TreeGraphs
(Journal article; Peer reviewed, 2020)We investigate the parameterized complexity of the recognition problem for the proper Hgraphs. The Hgraphs are the intersection graphs of connected subgraphs of a subdivision of a multigraph H, and the properness means ... 
Reconstructing ribosomal genes from large scale total RNA metatranscriptomic data
(Journal article; Peer reviewed, 20200313)Motivation Technological advances in metatranscriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ metatranscriptomics, sequencing of total reverse transcribed ... 
Recursive TimeFrequency Reassignment
(Master thesis, 20081118)A fast algorithm for producing timefrequency representations (TFRs) is proposed. The resulting TFRs have optional timefrequency resolution up to optimality. The algorithm is further extended with a method known as ... 
Reducing Graph Transversals via Edge Contractions
(Journal article; Peer reviewed, 2020)For a graph parameter π, the Contraction(π) problem consists in, given a graph G and two positive integers k,d, deciding whether one can contract at most k edges of G to obtain a graph in which π has dropped by at least ... 
Refined Complexity of PCA with Outliers
(Conference object; Peer reviewed; Journal article, 2019)Principal component analysis (PCA) is one of the most fundamental procedures in exploratory data analysis and is the basic step in applications ranging from quantitative finance and bioinformatics to image analysis and ... 
Refined notions of parameterized enumeration kernels with applications to matching cut enumeration
(Journal article; Peer reviewed, 2021)An enumeration kernel as defined by Creignou et al. (2017) [11] for a parameterized enumeration problem consists of an algorithm that transforms each instance into one whose size is bounded by the parameter plus a ... 
Reflections on Courses for Software Language Engineering
(Conference object; Peer reviewed, 2014)Software Language Engineering (SLE) has emerged as a field in computer science research and software engineering, but it has yet to become entrenched as part of the standard curriculum at universities. Many places have a ... 
Regular Expressions with Numerical Constraints and Automata with Counters
(Lecture Notes in Computer Science, Chapter; Peer reviewed, 2009)Regular expressions with numerical constraints are an extension of regular expressions, allowing to bound numerically the number of times that a subexpression should be matched. Expressions in this extension describe the ... 
Regulatory mechanisms of noncoding RNAs during zebrafish embryogenesis
(Doctoral thesis; Peer reviewed, 20130503)For many years, RNAs were thought to be intermediate products between DNA and protein. The discovery of RNA interference (RNAi), a regulatory process that uses small noncoding RNAs to regulate gene expression at the ... 
Relation between oequivalence and EAequivalence for Niho bent functions
(Journal article; Peer reviewed, 2021)Boolean functions, and bent functions in particular, are considered up to socalled EAequivalence, which is the most general known equivalence relation preserving bentness of functions. However, for a special type of bent ... 
Relative Persistent Homology
(Journal article; Peer reviewed, 2020)The alpha complex efficiently computes persistent homology of a point cloud X in Euclidean space when the dimension d is low. Given a subset A of X, relative persistent homology can be computed as the persistent homology ... 
Reliable Asynchronous Communication in Distributed Systems
(Master thesis, 20180411) 
Repeats and EST analysis for new organisms
(Journal article, 20080118)Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask ... 
Restricted maximumlikelihood method for learning latent variance components in gene expression data with known and unknown confounders
(Journal article; Peer reviewed, 2022)Random effects models are popular statistical models for detecting and correcting spurious sample correlations due to hidden confounders in genomewide gene expression data. In applications where some confounding factors ...