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Randomised Construction and Dynamic Decoding of LDPC Codes
(Master thesis, 2005-11-30) -
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 long-standing, notorious open problem in parameterized complexity. Some years ago, the breakthrough work by Kratsch and ... -
Rapid genome editing by CRISPR-Cas9-POLD3 fusion
(Journal article; Peer reviewed, 2021)Precision CRISPR gene editing relies on the cellular homology-directed 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 RNA-Seq analysis workflow with Snakemake
(Journal article; Peer reviewed, 2020)Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq ... -
Rate and power allocation for discrete-rate link adaptation
(Peer reviewed; Journal article, 2008-01-09)Link adaptation, in particular adaptive coded modulation (ACM), is a promising tool for bandwidth-efficient transmission in a fading environment. The main motivation behind employing ACM schemes is to improve the spectral ... -
(Re)packing Equal Disks into Rectangle
(Journal article; Peer reviewed, 2022)The problem of packing of equal disks (or circles) into a rectangle is a fundamental geometric problem. (By a packing here we mean an arrangement of disks in a rectangle without overlapping.) We consider the following ... -
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
(Journal article; Peer reviewed, 2020-11)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 Tree-Graphs
(Journal article; Peer reviewed, 2020)We investigate the parameterized complexity of the recognition problem for the proper H-graphs. The H-graphs are the intersection graphs of connected subgraphs of a subdivision of a multigraph H, and the properness means ... -
Recommendations for Identifying Valid Wear for Consumer-Level Wrist-Worn Activity Trackers and Acceptability of Extended Device Deployment in Children
(Journal article; Peer reviewed, 2022)Background: Self-reported physical activity is often inaccurate. Wearable devices utilizing multiple sensors are now widespread. The aim of this study was to determine acceptability of Fitbit Charge HR for children and ... -
Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
(Journal article; Peer reviewed, 2020-03-13)Motivation Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ meta-transcriptomics, sequencing of total reverse transcribed ... -
Recursive Time-Frequency Reassignment
(Master thesis, 2008-11-18)A fast algorithm for producing time-frequency representations (TFRs) is proposed. The resulting TFRs have optional time-frequency 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 ... -
Refactoring of Ocean Data Processing and Visualization Software Using Scientific Workflow Modeling
(Master thesis, 2021-06-01)The Arctic Package is a MATLAB software package for modeling and visualization of acoustic propagation. It aims to improve the accessibility and understanding of ocean processes and how they affect the climate. This thesis ... -
Refined Complexity of PCA with Outliers
(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
(Journal article; 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 ... -
Regulation of defective mitochondrial DNA accumulation and transmission in C. elegans by the programmed cell death and aging pathways
(Journal article; Peer reviewed, 2023)The heteroplasmic state of eukaryotic cells allows for cryptic accumulation of defective mitochondrial genomes (mtDNA). ‘Purifying selection’ mechanisms operate to remove such dysfunctional mtDNAs. We found that activators ... -
Regulatory mechanisms of non-coding RNAs during zebrafish embryogenesis
(Doctoral thesis, 2013-05-03)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 non-coding RNAs to regulate gene expression at the ... -
Reinforcement Learning for Lifelong Multi-Agent Pathfinding in AutoStore system
(Master thesis, 2023-05-25)AutoStore (AS) uses a cubic system for warehouse automation, utilizing robots to retrieve and organize objects in a three-dimensional grid of bins in a Manhattan geometry environment. Lifelong Multi-Agent Pathfinding (LMAPF) ...