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QALM  a tool for automating quantitative analysis of LCMSMS/MS data
(Master thesis, 20100531)The goal of bioinformatics is to support science and research in the field of biology through the application of information technology. Proteomics is a field within biology that deals with the study of proteins. This paper ... 
Quantitative Externalization of Visual Data Analysis Results Using Local Regression Models
(Journal article; Peer reviewed, 2017)Both interactive visualization and computational analysis methods are useful for data studies and an integration of both approaches is promising to successfully combine the benefits of both methodologies. In interactive ... 
Quantitative transcriptomics, and lipidomics in evaluating ovarian developmental effects in Atlantic cod (Gadus morhua) caged at a capped marine waste disposal site
(Journal article; Peer reviewed, 2020)In the present study, a previously capped waste disposal site at Kollevåg (Norway) was selected to study the effects of contaminant leakage on biomarkers associated with Atlantic cod (Gadus morhua) reproductive endocrinology ... 
Quantum social networks
(Peer reviewed; Journal article, 20120627)We introduce a physical approach to social networks (SNs) in which each actor is characterized by a yes–no test on a physical system. This allows us to consider SNs beyond those originated by interactions based on preexisting ... 
Quick but odd growth of cacti
(Conference object; Peer reviewed; Journal article, 2015)Let F be a family of graphs. Given an input graph G and a positive integer k, testing whether G has a ksized subset of vertices S, such that G\S belongs to F, is a prototype vertex deletion problem. These type of problems ... 
Quick separation in chordal and split graphs
(Journal article; Peer reviewed, 2020)In this paper we study two classical cut problems, namely Multicut and Multiway Cut on chordal graphs and split graphs. In the Multicut problem, the input is a graph G, a collection of 𝓁 vertex pairs (si, ti), i ∈ [𝓁], ... 
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 ... 
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 ... 
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 ... 
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 ...