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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 ... 
Ridge Extraction, and Illustrative Visualization of an FTLE Flow Field.
(Master thesis, 20120601)Illustrative visualization of a flow is an area that is proving to be interesting and in later years something that have been somewhat explored, it can provide some very interesting results and in this thesis we find the ... 
Risks in Networked Computer Systems
(Doctoral thesis, 20080924)Networked computer systems yield great value to businesses and governments, but also create risks. The eight papers in this thesis highlight vulnerabilities in computer systems that lead to security and privacy risks. A ... 
Robust CrossPlatform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis
(Peer reviewed; Journal article, 201709)Information integration and workflow technologies for data analysis have always been major fields of investigation in bioinformatics. A range of popular workflow suites are available to support analyses in computational ... 
Robust Independent Validation of Experiment and Theory: Rivet version 3
(Journal article; Peer reviewed, 2020)First released in 2010, the Rivet library forms an important repository for analysis code, facilitating comparisons between measurements of the final state in particle collisions and theoretical calculations of those final ... 
The Role of Humans in Complex ICT Systems
(Master thesis, 20161016)In the modern world, companies, regardless of their type of business, rely on information and communications technology (ICT) systems to carry out their everyday operations. The ICT systems have been developed over time ...