• QALM - a tool for automating quantitative analysis of LC-MS-MS/MS data 

      Lerøy, Kjartan (Master thesis, 2010-05-31)
      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 

      Matkovic, Kresimir; Abraham, Hrvoje; Jelovic, Mario; Hauser, Helwig (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 

      Khan, Essa Ahsan; Zhang, Xiaokang; Hanna, Eileen Marie; Bartosova, Zdenka; Yadetie, Fekadu; Jonassen, Inge; Goksøyr, Anders; Arukwe, Augustine (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 

      Cabello, Adán; Danielsen, Lars Eirik; López-Tarrida, Antonio J.; Portillo, José R. (Peer reviewed; Journal article, 2012-06-27)
      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 pre-existing ...
    • Quick but odd growth of cacti 

      Kolay, Sudeshna; Lokshtanov, Daniel; Panolan, Fahad; Saurabh, Saket (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 k-sized 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 

      Misra, Pranabendu; Panolan, Fahad; Rai, Ashutosh; Saurabh, Saket; Sharma, Roohani (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 

      Knudsen, Joakim Grahl (Master thesis, 2005-11-30)
    • Rank vertex cover as a natural problem for algebraic compression 

      Meesum, Syed Mohammad; Panolan, Fahad; Saurabh, Saket; Zehavi, Meirav (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 

      Reint, Ganna; Li, Zhuokun; Labun, Kornel; Keskitalo, Salla; Soppa, Inkeri; Mamia, Katariina Aino Inkeri; Tolo, Eero; Szymanska, Monika; Meza-Zepeda, Leonardo A.; Lorenz, Susanne; Cieslar-Pobuda, Artur Grzegorz; Hu, Xian; Bodin, Diana L; Staerk, Judith; Valen, Eivind Dale; Schmierer, Bernhard; Varjosalo, Markku; Taipale, Jussi; Haapaniemi, Emma Maria (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 

      Zhang, Xiaokang; Jonassen, Inge (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 

      Gjendemsjø, Anders; Øien, Geir Egil; Holm, Henrik; Alouini, Mohamed-Slim; Gesbert, David; Hole, Kjell Jørgen; Orten, Pål (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 ...
    • ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species 

      Hanna, Eileen Marie; Zhang, Xiaokang; Eide, Marta; Fallahi, Shirin; Furmanek, Tomasz; Yadetie, Fekadu; Zielinski, Daniel Craig; Goksøyr, Anders; Jonassen, Inge (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 

      Chaplick, Steven; Golovach, Petr; Hartmann, Tim; Knop, Dusan (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 ...
    • Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data 

      Xue, Yaxin; Lanzén, Anders; Jonassen, Inge (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 

      Nilsen, Geir Kjetil (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 

      Lima, Paloma T.; dos Santos, Vinicius F.; Sau, Ignasi; Souza, Uéverton S. (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 

      Fomin, Fedor; Golovach, Petr; Panolan, Fahad; Simonov, Kirill (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 

      Golovach, Petr; Komusiewicz, Christian; Kratsch, Dieter; Le, Van Bang (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 

      Bagge, Anya Helene; Lämmel, Ralf; Zaytsev, Vadim (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 

      Hovland, Dag (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 ...